Data from: Molecular detection and phylogenetic characterization of <em>Wolbachia</em> strains in <em>Glossina</em> species from Nigerian conservation areas

Tsetse flies (Glossina spp.), the vectors of human and animal African trypanosomiasis, continue to exert a profound toll on public health and livestock productivity in Nigeria. This study investigates the prevalence, seasonal dynamics, and genetic diversity of Wolbachia endosymbionts in 7,632 wild-caught tsetse flies sampled from four ecologically distinct conservation sites: Yankari Game Reserve, Kainji Lake National Park, Kagarko Forest, and Ijah Gwari Forest. Molecular screening based on wsp gene sequencing detected Wolbachia in 1,771 flies, with infection rates rising significantly during the wet season (e.g., G. morsitans submorsitans: 75.4% vs. 39.8% in dry season; p &lt; 0.001). Female flies showed consistently higher infection prevalence, reinforcing the role of vertical transmission. Phylogenetic reconstruction revealed nine Wolbachia strains spanning supergroups A and B, including a putatively unique regional variant (wsp9) restricted to northern Nigeria. Bacterial load exhibited a strong age-dependent pattern (r = 0.912, p &lt; 0.001), and elevated GC content (~63%) suggested possible adaptation to savanna thermal conditions. These findings highlight the ecological flexibility of Wolbachia within natural tsetse populations and point to its potential application in vector control—particularly through mechanisms like cytoplasmic incompatibility. By combining molecular detection, ecological data, and evolutionary analysis, this study lays the groundwork for tailored, climate-sensitive Wolbachia-based strategies to reduce tsetse populations and support trypanosomiasis control in Nigeria.