Population Genetic Structure Analysis of Red-Spotted Grouper in Western Japan based on SNPs

Red-spotted grouper Epinephelus akaara, a commercially valuable fish, has recently been included among the target species for stock assessment in Japan. However, its population genetic structure along Japanese coastal waters remains unclear. This study aimed to unveil the population genetic structure of E. akaara along the western Japanese coast based on nuclear single-nucleotide polymorphisms (SNPs). A total of 176 individuals were collected from six locations across four marine regions: the East China Sea (Kagoshima and Nagasaki Prefectures), the Sea of Japan (Shimane and Toyama Prefectures), the Seto Inland Sea (Hiroshima Prefecture), and the Pacific Ocean (Aichi Prefecture). Sequence data were obtained by degenerate oligonucleotide primer MIG-seq (dpMIG-seq), and SNPs were identified by de novo analysis. Genetic diversity within each population was evaluated based on expected heterozygosity (H_E). Population genetic structure was assessed by pairwise F_ST values, analysis of molecular variance (AMOVA), ADMIXTURE, principal component analysis (PCA), and maximum-likelihood phylogeny. All populations exhibited comparable levels of H_E. Pairwise F_ST values were extremely low, and AMOVA showed that 99.75% of the genetic variation was explained by within-population variation. Cross-validation error (K) in the ADMIXTURE analysis converged towards 1. Neither PCA nor the maximum-likelihood tree showed population-specific clustering. SNP analysis suggested no genetic population structure in E. akaara along western Japan. This species has a pelagic duration of approximately one month during its egg through larval stages. Therefore, oceanographic dispersal may promote gene flow in the pelagic stage and thereby limits population differentiation. In addition, considering the long generation time due to its longevity, substantial population differentiation might not have developed after the final postglacial reconnection of the waters surrounding Japan.