This study was carried out to determine the molecular characterization of simuliid species which cause a problem in the part of Kızılırmak passes from Ürgüp and Gülşehir districts of Nevşehir. Between May and September 2011, totally 150 simuliid larvae were sampled. Morphological identifications of the collected larvae specimens were done before the molecular analyses. Genomic DNA extractions were utilized on 7 larvae specimens which were selected from morphologically identified samples and the sequence and phylogenetic analyses were performed after the amplification of the partial mitochondrial cytochrome oxidase subunit 1 (mt-COI) and ribosomal complete internal transcript spacer 2 and partial 28S (ITS-2/28S) gene regions. Eighty-five, 46 and 19 out of 150 morphologically examined specimens were identified as Simulium (S.) Wilhelmia sp., S. Wilhelmia lineatum and S. Wilhelmia balcanicum, respectively. Among the amplified samples with respect to mt-COI and ITS-2/28S gene regions, sequence analyses were performed on 3 and 2 isolates from S. Wilhelmia sp. and both S. lineatum and S. balcanicum. The isolates were found to be clustered together depending on the species for both gene regions phylogenetically and the sequence heterogeneity was found to be higher in S. lineatum. When comparing with the other species under the Wilhelmia subgenus, S. lineatum and S. balcanicum were determined to be more close to each other. Scientific data on the molecular characterization and phylogeny of blackfly species under the S. Wilhelima subgenus which pose a problem in the Central Kızılırmak Basin were provided with this study.
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