Genetic Diversity of Penaeus monodon (Fabricius, 1798) in the Philippines as Revealed by Mitochondrial Cytochrome Oxidase I (COI)

The mitochondrial cytochrome oxidase I (COI) marker, widely used in phylogenetic and DNA barcoding studies, may also be informative with respect to intraspecies diversity and regional scale population structure. It is particularly useful when data reported from other studies and relevant for comparative studies were mostly generated using this marker. In this study, the COI marker was used to investigate the genetic diversity and structure of populations of the black tiger shrimp, Penaeus monodon (Fabricius, 1798), in the Philippines. Wild specimens were obtained from six locations across the Philippine archipelago. Among the 146 COI sequences observed, only 15 haplotypes were identified of which only three were found to be frequent and widely distributed and the others were either unique to a site, or found in only two sites. The COI sequences therefore indicated that the six sites did not show significant genetic differentiation based on the Chi-square test, analysis of molecular variance (AMOVA), and FST analysis. However, comparison of the data with those reported for Thailand revealed that the Philippine populations have significantly lower haplotype and nucleotide diversity. The three widely distributed haplotypes in the Philippines were also observed in Thailand; these three haplotypes appeared to be the ancestral forms as suggested by the haplotype network analysis. The Philippine haplotypes showed less sequence divergence among themselves and clustered mostly in one major lineage of the tree, although two haplotypes were found to be highly divergent and clustered with other Thai haplotypes. The genetic diversity discovered in the study represents a significant resource; it also highlights opportunities for selection of better performing stocks.