Genome-Wide Genetic Diversity and Population Structure of Sillago sinica (Perciformes, Sillaginidae) from the Coastal Waters of China: Implications for Phylogeographic Pattern and Fishery Management

The ability to detect population structure and determine the extent of genetic variation among populations is critical for understanding genetic background and effective fishery management. Fifty-eight individuals of <i>S. sinica</i> were resequenced with an average depth of 24× based on the Illumina sequencing platform. A total of 7,409,691 high-quality single nucleotide polymorphisms (SNPs) and 327,698 linkage disequilibrium-pruned SNPs were detected by comparing with the reference genome, and the average nucleotide diversity (<i>π</i>) and polymorphism information content (<i>PIC</i>) for all SNPs were 0.0036 ± 0.0023 and 0.2358 ± 0.1013, respectively, indicating the relatively low level of genetic diversity caused by limited gene flow and small effective population size (<i>N</i>_e). Integrated analyses of principal component analysis (PCA), ADMIXTURE, fixation index (<i>F</i>_st), and cladogram showed a significant genetic divergence between the north group (Dongying and Rushan populations) and the south group (Wenzhou and Zhoushan populations), which might be related to the differences in natural and geographical environments. The comprehensive results confirmed the genetic heterogeneity of <i>S. sinica</i> populations from the northern and southern sea areas of China, and suggested that regionalization fishery management should be adopted for further resource protection and utilization of <i>S. sinica</i>.