• Journal of Aquaculture
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• v.22 no.1
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• pp.83-91
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• 2009

The Korean doty barbel Hemibarbus mylodon (Cypriniformes; Cyprinidae) is a critically endangered freshwater fish species mainly because of its natural habitat degradation. Three full-length complementary DNA (cDNA) clones representing different muscle actin isoforms were isolated and characterized. The three muscle actin isoforms were 1,294-1,601 bp long with the identical open reading frames of 1,134 bp with the deduced amino acid residues of 377. They showed 83.9-87.2% identities in the coding nucleotide level and 96.8-98.1% identities in the amino acid level. Phylogenetic analysis with the coding nucleotide sequences revealed that three muscle actin isoforms of H. mylodon formed strongly supported monophyletic groups with one of cypriniform skeletal $\alpha$-actin (acta1), cypriniform aortic $\alpha$-actins (acta2), and uncharacterized Danio rerio muscle actin isoform/Salmo trutta slow muscle actin (a novel muscle actin type). Our phylogenetic tree further suggested that cypriniform acta2 only showed the orthologous relationship to tetrapod acta2. Other multiple actin isoforms from diverse teleostean taxa were however clustered to no tetrapod orthologs, i.e., acta1, cardiac $\alpha$-actins (aetc1), acta2, and enteric $\gamma$-actin (actg2). This result strongly suggested that teleostean muscle actins have experienced different and complicated evolutionary history in comparison to mammalian counterparts.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.199-208
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• 2021

Environmental DNA (eDNA) metabarcoding is effective method with high detection sensitivity for evaluating fish biodiversity and detecting endangered fish from natural water samples. We compared the richness of operational taxonomic units(OTUs) and composition of freshwater fishes according to filters(cellulose nitrate filter vs. glass fiber filter), extraction kits(DNeasy2^® Blood & Tissue Kit vs. DNeasy2^® PowerWater Kit), primer sets (12S rDNA vs. 16S rDNA), and PCR methods (conventional PCR vs. touchdown PCR) to determine the optimal conditions for metabarcoding analysis of Korean freshwater fish. The glass fiber filter and DNeasy2^® Blood & Tissue Kit combination showed the highest number of freshwater fish OTUs in both 12S and 16S rDNA. Among the four types, the primer sets only showed statistically significant difference in the average number of OTUs in class Actinopterygii (non-parametric Wilcoxon signed ranks test, p=0.005). However, there was no difference in the average number of OTUs in freshwater fish. The species composition also showed significant difference according to primer sets (PERMANOVA, Pseudo-F=6.9489, p=0.006), but no differences were observed in the other three types. The non-metric multidimensional scaling (NMDS) results revealed that species composition clustered together according to primer sets based on similarity of 65%; 16S rDNA primer set was mainly attributed to endangered species such as Microphysogobio koreensis and Pseudogobio brevicorpus. In contrast, the 12S rDNA primer set was mainly attributed to common species such as Zacco platypus and Coreoperca herzi. This study provides essential information on species diversity analysis using metabarcoding for environmental water samples obtained from rivers in Korea.

• Korean Journal of Ecology and Environment
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• v.53 no.2
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• pp.156-164
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• 2020

The accurate estimation of fish assemblages is highly dependent on the sampling gear used for sampling. We used data from 15 sampling sites along the Nakdong River, which is a large river in South Korea, to identify differences in assemblages and sizes of freshwater fishes collected with either cast nets or gill nets, the two most commonly used sampling gear in South Korea. The two gears differed in the fish assemblages they captured, with more species caught by gill nets. Further, due to its tighter mesh size, the cast net caught significantly smaller fishes than the gill nets(independent t-test, p<0.05). We found the cast net to be appropriate for species that inhabit shallow (less than 2 m) and open water, but inappropriate for deep water, habitats with plant beds, and nocturnal species. Thus, cast net sampling is not efficient in a large river environment, and a combination of sampling methods is more suitable for understanding fish assemblages in such habitats. In general, appropriate selection of fishing methods to specific habitats is necessary to improve data quality and minimize the misrepresentation of environmental conditions.

• Korean Journal of Ichthyology
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• v.31 no.4
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• pp.241-248
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• 2019

The freshwater fish fauna for the whole water system of Geogeumdo Island was surveyed at a total 10 sites from March 2018 to February 2019. During the surveyed period, 13 species belonging to 5 families and 4 orders were collected. Cyprinidae (68.84%) and Gobiidae (18.21%) were the dominant family, and the dominant species was Zacco temminckii (53.71%), and the subdominant species was Rhynchocypris oxycephalus (10.78%). Kichulchoia brevifasciata (1.27%) that endangered species were found in this study, but the habitat was confirmed in one site in Sinpyeongcheon compared to previous literature. Three endemic species of Korea were found in this island such as Iksookimia hugowolfeldi (5.07%), Liobagrus somjinensis (2.99%) and K. brevifasciata (1.27%). According to analysis of fish community structure based on average diversity, evenness index, dominance and richness indices in Geogeumdo Island were 1.666, 0.649, 0.645 and 1.713, respectively.

• Korean Journal of Ichthyology
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• v.34 no.3
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• pp.208-217
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• 2022

We wanted to develop a real-time PCR assay capable of detecting Liobagrus obesus in environmental DNA (eDNA) extracted from freshwater samples using a pair of species-specific primers and probe for the endangered fish, L. obesus. The species-specific primers and probe were designed in consideration of single nucleotide polymorphisms between 65 species of freshwater fish living in the Republic of Korea within the cytochrome b (cytb) gene of mitochondrial DNA. The species-specific primers and probe, in the real-time PCR assay, showed high specificity as only the L. obesus genomic DNA (gDNA) was found to be positive in the specificity verification using 65 species gDNA of freshwater fish in the Republic of Korea. In addition, in the detection limit analysis using the serial dilution concentrations of L. obesus gDNA, it was found that it was possible to detect up to 0.2 pg, showing high sensitivity. Afterwards, using the species-specific primers and probe, real-time PCR assay was performed on freshwater samples obtained from 8 stations in the mid-upper basin of Geum River. As a result, the cytb gene of L. obesus was detected in total 5 stations including all 3 stations where this species was collected at the time of field survey. Therefore, the species-specific primers and probe developed in present study, and the real-time PCR assay using them, can accurately detect the cytb gene of L. obesus from eDNA samples, which can be utilized to monitor the existing habitats of this species and to discover potential new habitats.

• Journal of Aquaculture
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• v.20 no.4
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• pp.248-254
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• 2007

Representative cDNA libraries were constructed from various tissue sources of Hemibarbus mylodon, an endangered freshwater fish species in Korea, for the mining of expressed sequence tags (ESTs). Randomized and non-normalized EST analysis was performed with 7 unidirectional cDNA libraries generated from brain, intestine, kidney, liver, muscle, ovary or testis. Of 3,383 ESTs in total, the number of singleton was 2,029, and 333 contigs containing 1,354 ESTs were assembled (percent of unigene = 70.0%). Abundantly expressed gene transcripts and broad clustering of putative gene function were tissue-specific in general, and the redundancy was also variable among those libraries. Over half of H. mylodon ESTs were matched with orthologues from other teleosts among which zebrafish gene sequences were the most frequent in those matches. This initial setting of EST libraries achieved in the present study would be a fundamental basis for the banking of gene resources from this endangered fish species.

• Korean Journal of Ecology and Environment
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• v.56 no.4
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• pp.406-413
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• 2023

Captive breeding and reintroduction are crucial strategies for conserving endangered species populations. However, fish raised in predator-free environments, show a lack of recognition of predationrelated stimuli such as chemical and visual signals. It is critical to recognize chemical signals from injured conspecifics, also known as alarm signals, and the order or shape of predators to indicate the spread of predation risk in the habitat. We conducted a laboratory experiment to determine and adjust the optimal exposure period to induce appropriate anti-predator behavior response to different types of stimuli (Chemical, Visual and Chemical+Visual) for the endangered species Microphysogobio rapidus. Our results demonstrate that predator avoidance behavior varies depending on the types of stimuli and the duration of predation risk exposure. First, the results showed captive-breed M. rapidus show lack of response against conspecific alarm signal (Chemical cue) before the predation risk exposure period and tend to increase response over predation risk exposure time. Second, response to predator (visual cue) tend to peak at 48 hours cumulative exposure, but show dramatic decrease after 72 hours cumulative exposure. Finally, response to the mixed cue (Chemical+visual) tend to peak prior to the predation risk exposure period and show reduced response during subsequent exposure periods. This experiment confirms the lack of responsiveness to conspecific alarm signals in captive-bred M. rapidus and the need for an optimal nature behavior enhancement program prior to release of endangered species. Furthermore, responsiveness to predator visual signal peak at 48 hours cumulative exposure, suggest an optimal predation risk exposure period of up to 48 hours.

• Korean Journal of Environment and Ecology
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• v.32 no.6
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• pp.603-617
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• 2018

This study surveyed the diversity and community characteristics of benthic macroinvertebrates and freshwater fish, which are the main animal classifications in a hydro ecosystem, from May to September 2017 in the western plains of the Demilitarized Zone (DMZ). The results showed a total of 125 species of benthic macroinvertebrates belonging to 66 families, 19 orders, and four phyla in the streams and wetlands. Among benthic macroinvertebrates, Coleoptera (27 spp.: 21.60%) was the largest group in terms of species richness followed by Odonata (26 spp.: 20.80%), non-Insecta (22 spp.: 17.60%), and Hemiptera (11 spp.: 8.80%) occupying in the lentic area. Of the feeding function groups (FFGs), predators (51 spp.: 56.67%) showed a relatively larger presence, indicating the dominance of hygrophilous invertebrates that usually inhabit the freshwater wetlands or ponds. Of the habitat oriented groups (HOGs), climbers (33 spp.: 24.44%) and burrowers (17 spp.: 12.59%) were the dominant groups. This observation is typical in a slow flowing habitat and can lead to the disturbance of the ecosystem due to cannibalism among predators. Cannibalism can be caused by stress induced by various population and environmental factors. For the ecosystem services benchmark (ESB) value, site 13 appeared to be the highest with 82 marks while other sites showed relatively lower rates and indices (III water quality class with ${\alpha}$-mesosaprobic). The analysis result of stability factors showed that almost all sites were evaluated to be the I characteristic group with high resilience and resistance or the III characteristic group that was sensitive to environmental disturbance and formed uneven and unstable communities. Of the freshwater fishes, 46 species (3,405 individuals) belonging to 39 families and 18 orders were identified in all the investigated sites. Among them, Cyprinidae (30 spp.: 65.2%) was the largest group, and Zacco koreanus was identified as the dominant species (728 individuals, 21.4%). The survey of freshwater fish communities found both stable communities (sites 7 and 13) with low dominant index (0.39) and high diversity index (2.29) and unstable communities (sites 2, 3, 8, and 10) in opposite tendency. This survey found five Korean endemic species, 17 species belonging to the export controlled species, two endangered species level II (Lethocerus deyrollei and Cybister chinensis), and rare species (Dytiscus marginalis czerskii) among benthic macroinvertebrates. The survey also found an invasive species, Ampullarius insularus, which was distributed throughout the whole area and thus can continuously disturb the ecosystem in the western plain area in the DMZ. Of freshwater fish, one natural monument (Hemibarbus mylodon) and three endangered species level II (Acheilognathus signifer, Gobiobotia macrocephalus, and G. brevibarba) were observed. The survey also found four introduced species (Pomacea canaliculate, Carassius cuvieri, Lepomis macrochirus, Micropterus salmoides) in the western DMZ area, indicating the need for the protection and conservation measures.

• Journal of Aquaculture
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• v.21 no.3
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• pp.196-200
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• 2008

Korean spotted barbel Hemibarbus mylodon, is an endangered and endemic freshwater species in the Korean peninsula. Amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity and population genetic structure of three populations (Bukhan, Namhan and Imjin-river). Fifteen AFLP primer pairs produced 795 products of which 135 were polymorphic(17%). Percentages of polymorphic bands were similar among the three populations, with accounting 11.9%, 11.1%, and 13.4% for Bukhan, Namhan and Imjin-river populations, respectively. An average genetic similarity among the three populations was 0.969. The average heterozygosity (0.033-0.040) and genetic diversity (0.036-0.043) were significantly low. Pairwise distance and fixation index analyses of three populations also suggested quite a low genetic differentiation one another. These results would provide a fundamental baseline data to develop the effective strategy for the management and restoration of this endangered fish species.

• Korean Journal of Ichthyology
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• v.29 no.3
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• pp.205-217
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• 2017

Fauna of freshwater fish and community structure were investigated at 24 stations in the Hoecheon Stream and some adjacent tributaries of the Nakdonggang River, Korea from July 2016 to August 2017. During the period 42 species and 4 types belonging to 32 genera and 11 families were collected. In this collection fishes of Cyprinidae were 24 species and 4 types, most numerous possessing 59.1% of all. There were 16 Korean endemic species including Acheilognathus yamatsutae and Odontobutis platycephala, 3 endangered species such as Pseudobagrus brevicorpus and Koreocobitis naktongensis (rank I) and Culter brevicauda (rank II) and 2 exotic species such as Micropterus salmoides and Lepomis macrochirus. Fish species transferred from other native rivers were 4 species including Opsariichthys uncirostris amurensis, Hemiculter eigenmanni, Odontobutis interrupta and Tridentiger brevispinis. Dominant species was Zacco koreanus NS type (19.2%) and sub-dominant species was Z. platypus R type (16.1%). The structure of fish community in the Hoecheon Stream was very stable and diverse in having diversity 2.91, evenness 0.77, dominance 0.35 and species richness 4.67. Fish community was divided into 4 groups such as upper, middle, midlower and lower reach group based on similarity among surveyed stations.