Cryptic Diversity and Genetic Variation in a Korean Endemic Freshwater Fish, the Korean Dark Chub ( Zacco koreanus ) Compared With Its Relative Zacco temminckii

ABSTRACT Species boundaries are not always straightforward, especially during early stages of divergence, when gene flow may still take place. The Korean dark chub Zacco koreanus , a widely distributed freshwater fish endemic to Korea, was recently classified as a species distinct from its congener Z. temminckii . However, morphological differences between the two species are ambiguous and genetic differences between and within species remain largely unexplored. In this study, using mitochondrial DNA cytochrome oxidase I (COI), control region (CR) and nine newly developed microsatellite loci, we determined phylogenetic relationships and population genetic structure of Z. koreanus among six geographically separated river basins in comparison with Z. temminckii . We found that Z. koreanus comprises relatively well‐separated mitochondrial clades associated with major river basins, and that some individuals morphologically identified as Z. koreanus were genetically assigned to Z. temminckii , suggesting the possibility of natural hybridization between the two species. Z. koreanus individuals from the Nakdong and Seomjin Rivers are the most closely related to Z. temminckii , and they probably represent cryptic species, as they showed a genetic distance of 2.2%~2.9%, although Z. koreanus had a distinct genetic structure. Comparisons of the whole mitogenomes from different rivers further suggest that the Nakdong and Seomjin River populations may represent divergent evolutionary lineages within Z. koreanus and possible cryptic diversity. The results of this study provide insight into understanding how Korean freshwater fishes have evolved in response to geographically isolated major rivers. The evolutionary mechanisms underpinning the cryptic species diversity in freshwater systems are worthy of further study.