Bactrocera zonata (Saunders) as one of the most devastating species of the genus Bactrocera is a notorious polyphagous fruit fly pest attacking lots of commercially important host plant species in many parts of the world including Iran. Despite economic importance, the population genetics of B. zonata have remained relatively unexplored in the country. In this study, the genetic structure, genetic diversity, and demographic history of this pest in Iran were investigated on the basis of cytochrome oxidase c subunit 1 (COI) sequences. A total of 21 haplotypes were identified from66 individuals collected from seven locations. Genetic diversity indices (number of haplotypes, haplotype diversity, and nucleotide diversity) revealed high genetic diversity without any isolation by distance among the geographic areas. An overall low level of genetic differentiation between populations revealed by genetic structure analysis reinforces the hypothesis of free movement of flies throughout the geographic areas. Non-significant correlation between genetic distances and geographic distances was an indication of a high level of gene flow among the studied populations of the pest. In addition, the recent population expansion following a recent past bottleneck could be a factor that might be contributed to the overall low level of the genetic structure.Mismatch distribution analysis as well as Tajima’s D and Fu’s FS tests strengthens the likelihood of a recent expanded population following a population bottleneck.

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