Genetic diversity of wild and cultured black tiger shrimp (Penaeus monodon) in the Philippines using microsatellites

Six microsatellites were used to study (1) the genetic diversity of wild <i>Penaeus monodon</i> shrimp from four geographic regions (Palawan, Quezon, Capiz and Negros Occidental-W) in the Philippines, and (2) its association with the status of mangroves and intensity of shrimp culture systems in these regions. Two cultured populations (Negros Occidental-C and Antique) were used for comparison. All six microsatellite loci were polymorphic. A total of 184 different alleles were found over all loci. The total number of alleles per locus ranged from 6 to 54, with allele size ranging from 159 base pairs (bp) to 400 bp. The observed heterozygosity of the six loci ranged from 0.47 to 1.00. The number of genotypes per locus ranged from 5 to 70. <i>F</i>_st values showed significant genetic differentiation among the four wild populations. Genetic differences between wild populations were also detected by pairwise comparison based on genotypic and allelic frequencies. Genetic differentiation among wild populations exhibited a positive correlation with mangrove status and intensity of culture systems at <i>P</i>=0.083. The Negros Occidental-W population, which originated from an area with the most severe mangrove loss and the most intensive culture systems, was the most significantly differentiated population. It also showed less genotypes per locus than the other three wild populations, suggesting a decrease in genetic diversity in this population. The population from Capiz, a province with a wide area of extensive culture ponds and few remaining secondary mangroves was the second most differentiated population. The Quezon population, which originated from an area with a few extensive culture ponds and less mangrove destruction, was not genetically different from the Palawan population, which was from a pristine site with mostly primary mangroves and no major aquaculture industry. The cultured populations showed less genetic diversity and were significantly different from the four wild populations based on pairwise <i>F</i>_st values and pairwise comparisons of allelic and genotypic frequencies. The results suggest that (a) there was a significant genetic differentiation among the wild <i>P. monodon</i> populations in the Philippines, and (b) the cultured populations were significantly differentiated from the natural populations. More replicate samples from each of the geographic regions are needed to conclusively determine the possibility of an association between genetic differentiation and the status of mangroves and/or intensity of shrimp culture systems.