Population genomic evidence for high genetic connectivity among populations of small yellow croaker (Larimichthys polyactis) in inshore waters of China

Genetic variation at the genomic level is important for identifying fish stock structure in the ocean. However, population genetic structure in marine fishes has been proposed to be highly limited, which might be attributed to fewer barriers to gene flow as well as large population sizes, resulting in relatively high levels of connectivity among populations. Population genomic approaches have increased the accessibility and resolution of population genetic data to make ecological inferences, which made it possible to detect previously unidentified structure and obtain more accurate estimates of demographic parameters in wild populations. Here, we used restriction-site associated DNA (RAD) sequencing to sample genome-wide single nucleotide polymorphisms (SNPs) of Larimichthys polyactis, a marine fish species of high ecological and commercial importance distributed in coast of East Asia. To assess range-wide patterns of population structure of L. polyactis, a total of 93 individuals were sampled from six geographic localities along the coast of China. Two final datasets were developed from the nuclear and the mitochondrial genomes, which consisted of 14, 194 SNPs and 15 SNPs respectively. Pairwise F-ST across sampling localities were not significant and most genetic variation was found within individuals rather than among populations within groups or among groups. Both clustering analyses and discriminant analysis failed to detect any population structure. Our findings demonstrated the persistence of high levels of genetic connectivity and a lack of population structure across sampling locations of L. polyactis in inshore waters of China.