LAUSR

Introduction Glossina spp. (Glossinidae), Tabanus spp. (Tabanidae), Ancala spp. (Tabanidae), Atylotus spp. (Tabanidae) and Stomoxys spp. (Muscidae) are important transmitting vectors of African animal trypanosomosis in sub-Saharan Africa. There is paucity of information on the distribution and identification of these flies in cattle settlements in southwest Nigeria. Methods The distribution patterns, genetic variations and diversities of dipteran flies in southwest Nigeria were described and identified using morphological and molecular analysis of the 28S rDNA gene. Results Of the 13,895 flies examined morphologically between April 2016 and March 2017, tabanids were identified [ Tabanus (0.34%), Ancala (0.03%), Atylotus (0.01%), Haematopota (0.014%) and Chrysops (0.11%)]. Two stomoxyine species were identified; Stomoxys niger niger Macquart (45.30%) and Stomoxys calcitrans Linnaeus (17.29%) and two Glossina spp. namely; Glossina p. gambiense Vanderplank, 1911 (0.46%) and Glossina tachinoides Westwood (0.51%) were identified. The identities were further confirmed in a BLAST search using their nucleotide sequences. The median-joining network of the 28S rDNA gene sequences indicated that fly species examined were genetically distinct. The apparent density of all the trapped flies was highest at a mean temperature of 26–28 ℃, humidity > 80% and rainfall of 150–220 mm/month. The distribution of flies was observed to increase as vegetation increased in density and decreased in areas with relatively high human population density (> 100/km 2 ). Conclusions The population indices of the 28S rDNA gene of the flies suggest that analysis of nuclear DNA fragments may provide more information on the molecular ecology of these flies. Characterising fly species and assessing their impact are essential in distribution and monitoring AAT spread.