Genetic diversity and population structure of Mierspenaeopsis hardwickii (Decapoda: penaeidae) along the coastal waters of Peninsular Malaysia based on the mitochondrial COI gene

Mierspenaeopsis hardwickii (Miers, 1878) is a commercially important penaeid shrimp widely distributed along the coastal waters of Peninsular Malaysia. Despite its economic significance, information on its population structure remains limited. This study investigated the genetic diversity and population structure of M. hardwickii using the mitochondrial cytochrome oxidase subunit 1 (COI) gene. A total of 108 individuals of M. hardwickii were collected from seven localities representing two geographical regions: the Strait of Malacca (SOM) and the South China Sea (SCS). Analysis of approximately 1,100 bp COI sequences revealed low haplotype diversity (h = 0.133–0.257) and low nucleotide diversity (π = 0.0003–0.0056) across the sampled populations. Analysis of molecular variance (AMOVA) revealed that 68.71% of the total genetic variation was attributable to differences between the SOM and SCS regions, indicating strong regional genetic differentiation. This finding was further supported by a high and significant overall ΦST value (ΦST = 0.6732, p < 0.001). Phylogenetic and haplotype network analyses revealed two geographically differentiated mitochondrial groups corresponding to the SOM and SCS regions. The observed genetic structure may reflect historical biogeographic processes associated with Quaternary sea-level fluctuations and the emergence of the Sunda Shelf as a barrier to gene flow. These findings provide important baseline information for fisheries management and support the precautionary consideration of the SOM and SCS populations as provisional management units.