Genetic Structure and Demographic History of Yellow Grouper (Epinephelus awoara) from the Coast of Southeastern Mainland China, Inferred by Mitochondrial, Nuclear and Microsatellite DNA Markers

The yellow grouper (Epinephelus awoara) is distributed in the West Pacific Ocean. Its genetic structure and demography were investigated using mitochondrial COI, Cyt b, the ND2 gene, the nuclear RyR3 gene, and 10 microsatellite DNA markers. A total of 120 individuals were collected from four locations along the coast of southeastern mainland China. High levels of haplotype diversity (0.968) were observed in mitochondrial DNA, and the average number of alleles ranged from 13.4 to 20.3 in microsatellite DNA data, which showed that all populations exhibited a high level of genetic diversity. Deficiency of heterozygosity was observed in all populations with positive FIS, showing that the characteristics of hermaphroditism might also be an underlying cause. The results of PCA, UPGMA clustering analysis and the significant genetic differentiation found in the Beibu Gulf population revealed the prevention of gene flow caused by the Qiongzhou Strait. The population of E. awoara also presented two major lineages, resulting in the appearance of the land bridge of the Taiwan Strait as a possible factor during the Pleistocene glaciation. Analysis of demographic history revealed that E. awoara underwent a reduction in effective population size in the past, followed by a single instantaneous increase in population size.