Phylogenetic relationships and population structure of Portunus pelagicus in the coastal waters of Malaysia inferred from mitochondrial DNA and microsatellites

The abundance of blue swimmer crabs, Portunus pelagicus throughout the Indo-West Pacific region makes it a valuable target species for fishery industry. The increasing demands of P. pelagicus have led to a growing interest on the broodstock selection of this particular crab species. This study examined the phylogenetic relationships, demographic history and population structure of P. pelagicus through sequence analyses of mitochondrial cytochrome c oxidase I (COI) gene (600 bp) as well as fragment analyses of four pairs of microsatellite loci. A total of 109 crab samples were collected from five different populations throughout the coastal areas of Malaysia. These include Perak (Pantai Remis and Kuala Sepetang), Johor (Pendas), Negeri Sembilan (Port Dickson), Terengganu (Besut) and Sarawak (Bako). In total, 15 haplotypes were obtained with 13 unique haplotypes and two shared haplotypes. The phylogenetic analyses via the Neighbour Joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods supported the monophyletic status between P. pelagicus and P. sanguinolentus with high bootstrap value (100%). All three phylogenetic trees revealed similar tree topologies with differences in the bootstrap values. The clustering of all P. pelagicus samples into a single clade suggested that this species possibly belonged to a single species. The genetic identity of P. pelagicus was further elucidated with low genetic distances among the haplotypes (0.2-1.7%) via mitochondrial analyses. Limited variations were found among the populations of P. pelagicus with high haplotype diversity and low nucleotide diversity detected within each population. No hybrid individual was discovered based on the genetic analyses of P. pelagicus from sympatric sampling locations. Low FST values obtained among these populations also clarified that these crabs were compatible for breeding programs. One interesting finding of this study was the sharing of haplotypes between samples from Sarawa