This study reports intense horn fly infestations of horses raised in an important wetland ecosystem, Sultan Marshes in Central Anatolia, Turkey. In total, seven horses raised together were found to be harbored over 500 flies per site of each animal. Totally, 376 fly specimens were collected from the horses by using the nets and were subjected to the laboratory for species identification. All flies were morphologically identified as the adults of Haematobia irritans. Partial fragments of mitochondrial cytochrome oxidase I (mt-COI) gene from totally 50 isolates were amplified for sequence and phylogenetic analyses. The mt-COI sequence analyses revealed no polymorphism among the isolates and explored a unique haplotype for H. irritans. A mean haplotype and nucleotide diversities of 0.8571 and 0.00695 were determined, respectively, within the COI data set of H. irritans, and newly characterized haplotype from Turkey exhibited a mean intraspecific genetic difference of 1.0 to the all published sequences of the isolates from several countries. COI data set also revealed a mean interspecific genetic difference of 1.7 between H. irritans and Haematobia exigua.
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