Genomic analyses indicate two blue swimmer crab species in Australia, evidence for natural interspecific hybridization and genetic structure within species with implications for fisheries management and stock enhancement

Blue swimmer crab species are widely distributed in Indian and west Pacific Oceans including the coastline around Australia and have been identified as potential candidates for stock enhancement. A recent taxonomic review revealed the presence of two blue swimmer crab species in Australia, namely Portunus armatus which is found around most of the Australian coastline, and Portunus pelagicus which is found in the northern coast where it is sympatric with P. armatus. It is important to understand population structure and genetic diversity of Portunus spp. to efficiently manage stocks. In the present study we investigated species classification and population structure of Portunus spp. in Australia using full and partial genomic information, namely mitochondrial COX1 gene sequences derived from whole genome sequencing and single nucleotide polymorphic (SNP) markers developed from partial genome sequencing. Blue swimmer crab samples were collected from the western (n = 52), northern (n = 17) and eastern (n = 110) coasts of Australia. Genetic diversity and population genetic structure were assessed for within and between region variation. Our genomic results indicated the presence of two blue swimmer crab species in Australia. One, namely, P. pelagicus was found only in Northern Territory (Darwin), and other, namely P. armatus was found around Australia. There was evidence of natural hybridisation between two species in Northern Territory (Darwin) where they were sympatric. P. armatus populations from the western, northern and eastern regions were genetically different although there were no significant genetic differences observed between the Queensland and New South Wales populations nor between the two neighbouring populations in Western Australia. Results found in the present study supports the view that the P. armatus populations in western, northern and eastern regions of Australia should be treated as at least three different stocks. A lack of genetic structuring along the eastern coast suggests blue swimmer crabs can be considered as a single stock along the sampled range at least in relation to fisheries enhancement, release programs and broodstock management.