Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene

Abstract In this study, the population genetic structure and historical demography of the blue swimming crab, Portunus pelagicus, from southeastern sea of China were investigated using cytochrome c oxidase subunit I (COI) gene of mitochondrion. A total of 889 bp segment of COI gene was sequenced, which showed a high haplotype diversity (0.6833–0.8142) and low nucleotide diversity (0.0021–0.0034). Among 30 haplotypes defined in this study, one (H1) was the most dominant (47.7%) and shared by each locality, while the majority (23) were rare and only existed in one individual. The AMOVA analysis revealed a limited population genetic structure, which suggested a high level of gene flow along the distribution areas of China. This conclusion was supported by the pairwise FST comparison values. The topology of the neighbour-joining tree constructed using 30 haplotypes from four localities presented two distinct clades (clade A and clade B). Meanwhile, three sequences of P. pelagicus downloaded from NCBI database showed a high-level divergence with the individuals collected in our study, which might form a new cryptical species. The individuals of clade B were cryptically embedded in the whole population, with a low frequency (7.7–24.2%), while clade A accounted for 75.8–92.3%. Neutrality tests and mismatch analyses suggested a late Pleistocene population expansion for both clade A (47,000–66,000 years ago) and clade B (74,000–100,000 years ago). This study should provide insight into phylogeny, population genetic structure, conservation genetics, and sustainable management of P. pelagicus.