Genetic differentiation of Portunus trituberculatus, the world's largest crab fishery, among its three main fishing areas

•The swimming crab P. trituberculatus is the world's largest crab fishery.•AFLP population genetics analyses were conducted among its main fishing areas.•Genetic diversity appears high in populations from its three main fishing areas.•Genetic differentiation occurs among populations from its three main fishing areas.•A genome-wide signal of population genetic differentiation was detected.

The swimming crab Portunus trituberculatus is the world's largest crab fishery, accounting for about one quarter of the crabs caught commercially worldwide. Most of the total catch of this crab (∼95%) occurs in China in three main fishing areas: East China Sea, Yellow Sea, and Bohai Sea. This fishery, however, is experiencing intense fishing pressure in these areas and overexploitation appears to be occurring. Information on the levels of population genetic differentiation of P. trituberculatus among its three main fishing areas is lacking, which is important for management and conservation of this fishery. Herein, we investigated this issue using Amplified Fragment Length Polymorphisms (AFLPs). We examined samples of P. trituberculatus from three localities representing each of the main fishing areas, which included 20 individuals per locality, and obtained 372 polymorphic AFLP loci. Our results indicate that heterozygosity (i.e., genetic diversity) is high in the three populations examined compared to other local and non-local crab fisheries that are exploited at a much lower scale. Genetic differentiation among these populations was detected in all population (FST and θ(II)) and individual cluster analyses (STRUCTURE, FLOCK, and AFLPOP) conducted, and with all datasets (i.e., including only putatively neutral loci, only putatively selected loci, and all loci). We discuss potential factors responsible for the observed genetic differentiation and suggest that each of the three main fishing areas should be considered a different management/conservation unit. Our results further add to the growing body of literature showing that loci under putative directional selection may have more power to detect genetic structure in marine species with extremely large populations sizes, high dispersal potential, and/or recently diverged populations. Nonetheless, genetic differentiation among populations, although weaker, was also detected with the putatively neutral loci dataset, indicating a genome-wide signal, and strengthening the conclusions inferred from the putatively selected loci.