Microphysogobio rapidus, an endemic cyprinid fish species found exclusively in Korea, has been identified in only two tributaries of the Nakdong River. The species predominantly occupies the near-gravel bottom waters within shallow sections of the middle and lower reaches of the river, characterized by swift currents. M. rapidus is currently recognized as a critically endangered species due to its distinct habitat preference, as well as the negative impacts of stream dam development and water environment pollution. In this study, we used 10 microsatellite markers to examine the genetic diversity of M. rapidus in the upper Nam (UN), lower Nam (LN), and Deokcheon Rivers (DC) in Korea, with a specific focus on assessment of the impact of dam development. Fish sampled from the UN and LN showed a greater average number of alleles and allelic richness (A = 18.3–18.4, A_R = 13.8) compared to those from DC (A = 11.8, A_R = 11.5). The observed heterozygosity among the fish examined ranged from H_O = 0.748 (LN) to 0.766 (DC). All three fish groups exhibited a significant departure from Hardy–Weinberg equilibrium (HWE) (p < 0.05). Despite having the largest effective population size (N_e = 175 and 157, respectively), the fish sampled from UN and LN showed the highest inbreeding coefficients (F_IS = 0.056–0.053, respectively), which were highly significant (p < 0.01). In contrast, the fish sampled from DC exhibited the smallest effective population size (N_e = 61) and showed an inbreeding coefficient close to zero (p > 0.05). BOTTLENECK analysis and estimated M-ratio values (0.341–0.372) revealed indications of past population size reduction in all fish groups examined. No significant genetic differentiation (F_ST < 0.05) was detected using the DAPC, STRUCTURE, and AMOVA among the fish studied. However, pairwise comparisons of F_ST between fish sampled from the Nam and Deokcheon Rivers revealed significant values (p < 0.001) ranging from 0.013 to 0.014. In addition, the closest genetic distance (0.026) was observed between UN and LN, while the greatest distance (0.087) was found between UN and DC. Analysis of gene flow rates among the fish examined indicated asymmetrical gene exchange within the Nam River, which was 31.51% in the downstream direction (from UN to LN), with a minimal gene flow rate (0.41%) in the upstream (from LN to UN) direction. The opposite trend was recorded between DC and LN, with a higher gene flow rate (29.74%) in the upstream direction compared to the downstream direction (0.12%). Our study highlighted the importance of implementing long-term conservation efforts focused on maintaining river integrity by removing water barriers such as weirs that impede fish migration and implementing active protection measures, such as aquaculture breeding and reasonable stocking practices, to preserve M. rapidus in the study area.

The endangered freshwater fish Gobiobotia brevibarba is endemic to Korea and threatened by habitat disturbance in major river systems. We investigated four wild populations from the Han River basin (IJR, BHR, NHR) and the Geum River basin (GR) using eleven microsatellite loci to assess genetic diversity, population structure, and contemporary gene flow. All populations showed relatively high genetic diversity (H_O = 0.709–0.800, H_E = 0.707–0.803) and no evidence of inbreeding, although bottleneck signals under the infinite allele mutation model were detected in IJR and BHR. Contemporary effective population size was large in IJR (N_e = 2463) and moderate in NHR (N_e = 467), whereas estimates for BHR and GR were imprecise. Genetic differentiation was very low within the Han River basin (F_ST = 0.009–0.027) but weak and significant between Han and Geum (F_ST = 0.085–0.096), and clustering analyses (STRUCTURE, DAPC, find.cluster) consistently supported K = 2, separating Han from Geum River. Gene flow analyses indicated extremely limited interbasin gene flow (<4%) but asymmetric contemporary migration from BHR into both IJR and NHR; all other migration rates were similarly low. These results show that G. brevibarba currently maintains high genetic diversity and two basin-level genetic clusters, underscoring the need to manage Han and Geum River populations as separate units and conserve riffle habitats and longitudinal connectivity.

Sebastes thompsoni is a cold-water rockfish of commercial and ecological value off the coast of Korea, requiring conservation management. We analyzed seven microsatellite loci to assess genetic diversity, population structure, and historical effective population size (N_e) of five populations obtained from the South and East Seas of Korea in 2018. The observed heterozygosity (H_O = 0.759–0.816) was higher than previously reported, and none of the STRUCTURE, DAPC, or AMOVA analyses detected geographic differentiation among samples from the South and East coasts of Korea, indicating a single population within these coasts. There was genetic flow between the five groups, with migration rates ranging from 4.1 to 19.11. However, the current N_e of all populations is estimated to be <1000, and VarEff-based reconstructions indicate a recent, severe bottleneck following an expansion approximately 600–1200 years ago (100–200 generations ago). This suggests that genetic diversity loss may persist in the future due to long-term habitat loss, fishing pressure, and ocean current fluctuations. Therefore, S. thompsoni should be established as a single management unit covering the Korean Peninsula coast, and habitat protection, overfishing control, genetic management type resource release using various mother and broodstock, and periodic genetic monitoring should be promoted. This study provides evidence to guide efforts to secure long-term genetic resilience and sustainable management of S. thompsoni in Korean coastal waters.

Liobagrus geumgangensis is a novel Korean fish species endemic to the Geumgang and Mangyeonggang River basins on the Korean Peninsula. During a survey of L. geumgangensis, the discovery of Liobagrus mediadiposalis as a potential threat prompted an investigation into L. geumgangensis genetic diversity and structure. Three populations of L. geumagangensis and one population of L. mediadiposalis were investigated using a 1024-bp sequence in the cytb region of mitochondrial DNA. The Mangyeonggang River of L. geumagangensis displayed the lowest haplotype diversity (H_d) within a range of 0.000–0.337, with one to two haplotypes (h). The Jecheon region of the Geumgang River for L. geumagangensis population had the highest nucleotide diversity (π) and was within the range of 0.00000–0.00066. The h of L. mediadiposalis population was 3, the range of H_d was 0.292, and π was 0.00231. Tajima’s D (D) and Fu’s Fs (F) were negative and non-significant in the LgGJ population. The genetic structure of L. geumgangensis had no shared haplotypes among the three populations. The discovery of L. mediadiposalis in the Geumgang River suggests the necessity of non-habitat conservation and population management of fish farms to conserve L. geumgangensis.

The Korean or hard-shelled mussel, Mytilus unguiculatus, previously known as Mytilus coruscus, is one of the most economically and ecologically important bivalves in South Korea. However, the population size of this species has drastically reduced owing to overharvesting and habitat shrinkage. Because its genetic information is poorly documented, we contributed, in this study, the genetic diversity and structural analyses of 246 adult samples of M. unguiculatus from seven populations along the coastal areas of the mainland and islands of South Korea using a microsatellite multiplex assay. Genetic diversity analyzed from eleven polymorphic microsatellite loci was consistently moderate (0.50–0.57) in all populations. No recent bottleneck was found, indicating that the number of the studied populations did not decrease to an extent that resulted in a reduction of genetic diversity. Additional tests did not reveal any genetic structure across them, possibly resulting from constant gene flow, strong dispersal of planktonic larvae, and genetic admixture between wild populations. These results suggest that M. unguiculatus populations along the coastal areas of South Korea should be managed as a single unit. Our study provides crucial information for future genetic monitoring, conservation management, and population restoration plan in preparation for the rapid decline in bivalve resources.

Mitochondrial genomes (mitogenomes) play a key role in species identification and phylogenetic studies due to their stable gene arrangements and evolutionary insights. Dryophytes flaviventris, classified in 2020 and closely related to D. suweonensis, lacks mitochondrial DNA data for differentiation. This gap hinders accurate species identification, highlighting the need for further genomic studies. The complete mitogenome size of two D. flaviventris were 18,616–18,617 bp and those for two D. suweonensis were 18,610–18,616 bp, the mitogenomes of the two species consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and a D-loop. Phylogenetic analysis confirmed that the mitochondrial DNA of all four individuals formed a monophyletic group, showing no genetic differentiation. As a result, the two species do not form distinct clades, and mitogenomes could not differentiate them, suggesting they are not reciprocally monophyletic. This study presents the first mitogenome data for D. flaviventris and provides valuable insights into tree frog taxonomy.