Using nine microsatellite loci, the genetic diversity of natural populations of Bactrocera occipitalis and B. philippinensis was investigated. Estimates of genetic diversity based on allele number (n a and n e ), heterozygosity (H o and H e ) and Shannon information index (I) revealed that the Cavite population was the most genetically diverse (n a = 18.56; n e = 12.88; H o = 0.58; H e = 0.89; I = 2.55) and Pangasinan was the least (n a = 7.89; n e = 8.94; H o = 0.34; H e = 0.87; I = 2.31). Among groups, the intermediates were the most genetically diverse (n a = 25.44; n e = 15.30; H o = 0.52; H e = 0.92; I = 2.85) and B. philippinensis was the least (n a = 17.44; H o = 0.44; H e = 0.90; I = 2.54). A low level of genetic diversity was detected among populations. Pangasinan and Palawan populations were the most related while Palawan and Guimaras populations were the least. Among groups, B. occipitalis and intermediates were the most related while B. occipitalis and B. philippinesis were the least. Dendrogram analysis indicated that B. occipitalis, B. philippinensis, and intermediates are not genetically distinct from each other.
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