Population structure and genetic diversity of the endangered fish black shinner Pseudopungtungia nigra (Cyprinidae) in Korea: a wild and restoration population

Abstract

The black shinner Pseudopungtungia nigra Mori, 1935 is an endangered fish endemic to Korea. It lives in the narrow basin of the Geumgang River, Mangyeonggang River, and Ungcheoncheon Stream, which flow into the West Sea of Korea. One population of P. nigra in Ungcheoncheon Stream has been locally exterminated once; it is now inhabiting the upper reaches of the dam through a restoration program. Efforts to identify and understand the genetic structure of these populations are important for conservation planning. Here, we analyzed genetic diversity using 21 microsatellite markers for 9 populations. The mean number of alleles ranged from 4.4 to 8.1, mean allelic richness ranged from 4.6 to 7.8, mean observed heterozygosity ranged from 0.519 to 0.702, and mean expected heterozygosity ranged from 0.540 to 0.763. All groups had recent and historical bottlenecks (P < 0.05, M-ratio < 0.68). Three groups [YD (2019), OC and UC] had significant inbreeding index values, suggesting that they were engaged in inbreeding. We observed a moderate level of genetic differentiation between MG and the rest of the population (FST = 0.135 to 0.168, P < 0.05). The genetic structure exhibited a fitting constant K = 2, along with separation between MG and the remaining populations. With respect to genetic flow, YD (2019), OC, CG, and ND shifted to the UC population (0.263 to 0.278). The genetic flow of each population was transferred only within the population; there was no gene flow among populations, except for the Ungcheoncheon Stream population. This study shows that the Ungcheoncheon Stream population needs conservation efforts to increase its genetic diversity, and the Geumgang River populations needs a conservation plan that considers the possibility of conservation and evolution through gene exchange among the populations.

Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly

“…The whole genome sequence is basically your genetic heritage [ 23 ]. This heritage is very important as a basis for applying genome-wide research, microsatellite marker development, and population genetic studies [ 4 , 11 , 23 ].…”

“…Korean rose bitterling R. uyekii is endemic in the Republic of Korea and a common freshwater fish that inhabits rivers and tributaries such as Geumgang, Mangyeong, Yeongsan, Seomjin, and Tamjingang rivers in the Honamkwon region [ 1 ]. This region accommodates genetic and species differentiation, including significant genetic differentiation between the Geumgang and Mankyungang Rivers in Pseudopungtungia nigra , new speciation of Acheilognathus somjinensis between genera Acheilognathus, the discovery of a new species of Kichulchoia brevifasciata , Liobagrus geumgangensis , and the genetic structure of the species in the genus Coreoleuciscus [ 4 , 5 , 6 , 7 , 8 ]. These regions are considered high-diversity hotspot areas.…”

“…Therefore, uncovering the genetic structure of the species distributed in the Honamkwon region is important in evolutionary and genetic terms. In particular, given the significant genetic differentiation between the Geumgang and Mangyeonggang River populations of Pseudopungtungia nigra , it is expected that genetic differentiation has also occurred in populations between the Mangyeonggang and Geumgang River species of R. uyekii [ 4 ].…”

Assessment of the Genetic Diversity and Structure of the Korean Endemic Freshwater Fish Microphysogobio longidorsalis (Gobioninae) Using Microsatellite Markers: A First Glance from Population Genetics

“…Microsatellites have been mainly reported in studies on the genetic structure and diversity of the Gobioninae subfamily. Consequently, significant genetic diversity and structures were reported [20][21][22]. Microsatellites are commonly analyzed in population genetics studies because of their high intraspecific polymorphism and codominance [23,24].…”

Population structure of the critically endangered Brazilian guitarfish Pseudobatos horkelii (Rhinobatidae) revealed by double‐digest restriction site‐associated DNA sequencing

“…Genetic diversity can decrease as a result of genetic drift under limited gene flow and selection against poorly adapted genotypes (Davis & Shaw, 2001). In populations suffering from significant decline, consecutive bottlenecks or founder effects can result in genetic drift and inbreeding depression (Hallatschek & Nelson, 2010;Signorile et al, 2014;Willi et al, 2022;Kim et al, 2023). Thus, genetic diversity data for overfished species are an extremely important resource for conservation management.…”