Hybridization between two bitterling fish species in their sympatric range and a river where one species is native and the other is introduced.
ABSTRACT: The distributions of two bitterling fish (subfamily: Acheilognathinae), Tanakia lanceolata and T. limbata, overlap in western Japan. Acheilognathinae fish lay their eggs in the gills of freshwater bivalves, and the early juvenile stage develops in the gills. Populations of freshwater bivalves are declining worldwide, which has limited the number of spawning substrate for bitterlings. T. limbata has been artificially introduced to some rivers in Ehime, Japan, where it coexists with native T. lanceolata, and some hybrids have been observed. We collected both species from several sites in western Japan, and from the Kunichi River system in Ehime, and analyzed genetic population structure based on six microsatellite loci and sequences of the mitochondrial cytochrome b gene. Structure analysis identified three genetically distinct populations: T. lanceolata, T. limbata "West Kyushu", and T. limbata "Setouchi". Two clades of T. limbata were also supported by molecular phylogenetic analyses based on cytochrome b. Hybrids in Ehime originated mostly from interbreeding between male T. lanceolata and female T. limbata "West Kyushu", and made up 10.2% of all collected fish, suggesting that hybrids occurred frequently between females of colonizing species and males of native species. On the other hand, interspecific hybrids were detected at rates of 40.0%, 20.0%, and 17.6% in the Ima River (Fukuoka), Midori River (Kumamoto), and Kase River (Saga), respectively, which are naturally sympatric regions. We found a few T. limbata "Setouchi" in the Midori and Kase Rivers, which were supposed to be introduced from other regions, coexisting with native T. limbata "West Kyushu", and this cryptic invasion may have triggered the interspecific hybridization. These results suggest that artificial introduction of a fish species, a decline in the unionid population, and degradation of habitat have caused broad hybridization of bitterlings in western Japan.
Project description:Artificial transplantation of organisms and consequent invasive hybridization can lead to the extinction of native species. In Matsuyama, Japan, a native bitterling fish, Tanakia lanceolata, is known to form hybrids with another bitterling species, T. limbata, which was recently introduced from western Kyushu, Japan. These bitterlings spawn in the gills of two freshwater unionid species, Pronodularia japanensis and Nodularia douglasiae nipponensis, which have rapidly declined on the Matsuyama Plain in the past 30 years. To gauge the effect of invasive hybridization, we determined the genetic introgression between T. lanceolata and T. limbata and analyzed the morphology of these species and their hybrids to infer their niche overlap. We collected adult individuals of Tanakia spp. and genotyped them based on six microsatellite loci and mitochondrial cytochrome b sequences. We analyzed their meristic characters and body shapes by geometric morphometrics. We found that 10.9% of all individuals collected were hybrids. Whereas T. lanceolata were more densely distributed downstream and T. limbata were distributed upstream, their hybrids were widely distributed, covering the entire range of native T. lanceolata. The body height and anal fin length of T. limbata were greater than those of T. lanceolata, but their hybrids were highly morphologically variable, covering both parental morphs, and were widely distributed in the habitats of both parental species. Hybridization has occurred in both directions, but introduced T. limbata females and native T. lanceolata males are more likely to have crossed. This study shows that invasive hybridization with the introduced T. limbata is a potential threat to the native population of T. lanceolata via genetic introgression and replacement of its niche in streams.
Project description:Stocking hatchery fish can lead to disturbance and extinction of the local indigenous population. Masu salmon Oncorhynchus masou masou, which is endemic across Japan, is a commonly stocked fish for recreational fishing in Japan. To conserve the indigenous resource, their genetic information is required, however, especially on Kyushu Island, the paucity of genetic information for this species has hindered proper resource management. Here, to identify hatchery mitogenome haplotypes of this species, stocked in the Kase River system, Kyushu Island, Japan, and to provide mitogenomic information for the resource management of this species, we analyzed the whole-mitogenome of masu salmon in this river system and several hatcheries potentially used for stocking. Whole-mitogenome sequencing clearly identified hatchery haplotypes, like fingerprints: among the 21 whole-mitogenome haplotypes obtained, six were determined to be hatchery haplotypes. These hatchery haplotypes were distributed in 13 out of 17 sites, suggesting that informal stocking of O. m. masou has been performed widely across this river system. The population of no hatchery haplotypes mainly belonged to clade I, a clade not found in Hokkaido Island in previous studies. Sites without hatchery haplotypes, and the non-hatchery haplotypes in clade I might be candidates for conservation as putative indigenous resources. The whole-mitogenome haplotype analysis also clarified that the same reared strain was used in multiple hatcheries. Analysis of molecular variance suggested that stocked hatchery haplotypes reduce the genetic variation among populations in this river system. It will be necessary to pay attention to genetic fluctuations so that the resources of this river system will not deteriorate further. The single nucleotide polymorphism data obtained here could be used for resource management in this and other rivers: e.g., for monitoring of informal stocking and stocked hatchery fishes, and/or putative indigenous resources.
Project description:Many studies have evaluated the ecological integrity of large-scale estuaries of continental rivers using biotic indicators such as fish, phytoplankton and benthic communities. However, few studies have focused on the river estuaries of small and medium rivers. Molluscan fauna data in large estuaries or in the estuaries of large rivers have been collected by the The National Census on River Environments (conducted by the Ministry of Land, Infrastructure, Transport and Tourism) or National Survey on the Natural Environment (conducted by the Ministry of Environment). On the other hand, molluscan fauna of small and medium rivers are managed by local governments and have rarely been investigated.This paper provides basic information on the molluscan fauna of 70 rivers in Kyushu, Japan, collected with the aim of conserving estuaries of small and medium rivers. In total, 37 families, 82 species and 21,827 individuals were collected. The data are all accessible from the document "A dataset of shellfish fauna sampled in estuaries of medium and small rivers in Kyushu, Japan (http://ipt.pensoft.net/resource.do?r=shellfishes_in_kyushu)". According to the Red Data Book published by the Japanese Ministry of Environment in 2018, 3 species were determined as Critically endangered and Endangered, 6 species were determined as Vulnerable and 13 species were determined as Near Threatened. The proportions of individuals classified as Critically endangered and Endangered from the total number of individuals were extremely low, but the proportions of Near Threatened individuals were high. Our results indicate that the risk of molluscan extinction in small- and medium-sized river estuaries in Kyushu is high and that immediate conservation is necessary.
Project description:This paper focuses on an overview of radioactive cesium 137 (quasi-Cs137 included Cs134) contamination of freshwater fish in Fukushima and eastern Japan based on the data published by the Fisheries Agency of the Japanese Government in 2011. In the area north and west of the Fukushima Nuclear plant, freshwater fish have been highly contaminated. For example, the mean of active cesium (quasi-Cs137) contamination of Ayu (Plecoglossus altivelis) is 2,657 Bq/kg at Mano River, 20-40 km north-west from the plant. Bioaccumulation is observed in the Agano river basin in Aizu sub-region, 70-150 km west from the plant. The active cesium (quasi-Cs137) contamination of carnivorous Salmondae is around 2 times higher than herbivorous Ayu. The extent of active cesium (quasi-Cs137) contamination of Ayu is observed in the entire eastern Japan. The some level of the contamination is recognized even in Shizuoka prefecture, 400 km south-west from the plant.
Project description:Jibom Jung, Jongwoo Jung, and Won Kim (2018) A phylogenetic study was conducted to investigate whether distinct genetic groups are present within the East Asian Pagurus minutus. In this study, 167 individuals of P. minutus were collected along the coasts of South Korea, east coast of Honshu, west coast of Kyushu, Okinawa Islands of Japan, and Taiwan. The collection of P. minutus was divided into three groups based on the differences in cytochrome c oxidase subunit I (COI) sequences and morphological and color characters: Major Group (MAG), Minor Group (MIG), and Taiwan-Okinawa Group (TOG). MAG commonly inhabits the entire coast of South Korea (except for the northeast coast), east coast of Honshu, and west coast of Kyushu in Japan. MIG predominantly inhabits the northeast coast of South Korea, while a small proportion inhabits the west coast of South Korea and west coast of Kyushu in Japan. TOG is restricted to Taiwan and the Okinawa Islands of Japan. The COI divergence among MAG, MIG, and TOG was larger than the minimum interspecific divergence of the other Pagurus species. Little ingroup COI divergences exist in the MAG and MIG, but distinct ingroup COI divergence is present between the two subgroups of TOG inhabiting Taiwan and Okinawa Islands. MAG, MIG, and TOG show minor differences among morphological characters. Each specimen of these three groups has distinguishing color patterns. These differences in molecular, morphological and color characters suggest that P. minutus are separated into three groups at the species level, and this subdivision of P. minutus shows that additional phylogenetic studies of other hermit crabs and common marine decapod species in East Asia are needed.
Project description:The Genji firefly, Luciola cruciata, is widely distributed throughout the major Japanese islands (Honshu, Shikoku, and Kyushu) and distinguished into two ecological types on the basis of the flash interval of the mate-seeking males (4-sec slow-flash or 2-sec fast-flash intervals). The boundary of the ecological types corresponds to the Fossa Magna, a great rupture zone that separates eastern and western Japan. Although the degree of genetic differentiation of the two types has been evaluated using allozyme and mitochondrial DNA sequence data, it has not been evaluated using genome-wide data. Based on the genome-wide data obtained using single-end restriction-site-associated DNA (RAD-Seq), principal component, gene-level phylogenetic tree, admixture, and Wright's fixation index analyses, we identified three phylogenetic groups in L. cruciata: East-Honshu, West-Honshu, and Kyushu. This grouping corresponds to the ecological types: East-Honshu to the slow-flash type and West-Honshu and Kyushu to the fast-flash type. Although introgression was exceptionally observed around adjacent or artificially transplanted areas, gene flow among the groups was almost absent in the natural populations. The phylogenetic tree under the coalescent model also evaluated differentiation among the East-Honshu, West-Honshu and Kyushu groups. Furthermore, because the distribution patterns of the three groups are consistent with the geological history of Japanese islands, a vicariant speciation scenario of L. cruciata is concluded. In addition, we identified genetic markers that can be used to distinguish the three genetic groups for genetic management of firefly transplantation in nature conservation and regeneration.
Project description:The p.R4810K (rs11273543, c.14429G > A) variant of the RNF213 gene is associated with increased risk of Moyamoya disease (MMD), which is an idiopathic progressive intracranial vascular steno-occlusive disease, in Asian populations. Numerous variant association studies for this MMD variant have been performed in Japan to date. Since another genetic study that utilized approximately 140,000 single nucleotide polymor (SNPs) has indicated that there still are genetic differences among mainland Japanese, there is a possibility that the variant distribution in patients with MMD and normal individuals varies between different Japanese regions. Additionally, the majority of variant association studies have used Sanger sequencing, which is labor-intensive, time-consuming, and costly. In this study, we analyzed the frequency of the variant genotype in patients with MMD and normal individuals in Kyushu using pyrosequencing, which is an accurate, cost-effective, and automated method. We found differences in the genotype frequencies in familial patients from Kyushu and normal populations in Tohoku compared with west Japan, which suggested that there were differences in the frequency of the variant among different regions in Japan.
Project description:Red sea bream, a popular fish resource in Korea and Japan, is being bred in fish farms of the two countries. It is hypothesized that the genomes of red sea bream are influenced by decades of artificial selection. This study investigates the impact of artificial selection on genomes of red sea bream. Whole genome sequencing was conducted for 40 samples of red sea bream either from Ehime, Nagasaki and Tongyeong fish farms or from the wild. Population stratification based on whole genome data was investigated and the genomic regions of fish farm populations under selection were identified using XP-EHH and relative nucleotide diversity. Gene ontology analysis revealed that different functions were enriched in different fish farms. In conclusion, this study highlights the difference between independently cultured red sea bream populations by showing that influence of artificial selection acted upon completely different genes related to different functions including metabolic and developmental processes.
Project description:The bacterium Flavobacterium psychrophilum is a serious problem for salmonid farming worldwide. This study investigates by multilocus sequence typing (MLST) the population structure of this pathogen in Japan where it is also a major concern for ayu, a popular game fish related to salmoniforms. A total of 34 isolates collected across the country and 80 isolates sampled in a single model river by electrofishing were genotyped. The data accounting for 15 fish species allowed identifying 35 distinct sequence types (ST) in Japan. These ST are distinct from those reported elsewhere, except for some ST found in rainbow trout and coho salmon, two fish that have been the subject of intensive international trade. The pattern of polymorphism is, however, strikingly similar across geographical scales (model river, Japan, world) in terms of the fraction of molecular variance linked to the fish host (~50%) and of pairwise nucleotide diversity between ST (~5 Kbp(-1)). These observations go against the hypothesis of a recent introduction of F. psychrophilum in Japan. Two findings were made that are important for disease control: 1) at least two independent F. psychrophilum lineages infect ayu and 2) co-infections of the same individual fish by different strains occur.
Project description:A comparison of the growth, hematological values, fatty acids, and gonadal and growth hormonal changes of river puffer, Takifugu obscurus, tiger puffer, T. rubripes, their hybrids (river puffer × tiger puffer) and hybrid triploids was performed during 3 months of their early growth period. Several features were observed during these 3 months: hybrids showed the highest levels of specific growth rate, 1.48%; hybrid triploids showed the smallest change in viscera fat (P<0.05), but GSI was not significantly different among groups (P>0.05). Considering hematological parameters, hybrid triploids had increased mean corpuscular volume and mean corpuscular hemoglobin (P<0.05), but other parameters were not significantly different between groups (P>0.05). With respect to fatty acids, puffer fish, hybrids and hybrid triploids contained fatty acids such as SFAs, MUFAs, n-3 PUFAs and n-6 PUFAs. There were significantly different amounts of total fatty acids between groups (P<0.05), however, rates of changes in fatty acids did not differ significantly between groups (P>0.05). Gonadal hormone (estradiol and testosterone) changes in the river puffer and tiger puffer were significantly higher than that observed in hybrids and hybrid triploids. The hybrids and tiger puffers had higher amounts of growth hormone (thyroid stimulating hormone and thyroxine) than the hybrid triploids and river puffers (P<0.05).