2.3. BvHV Sequence, Phylogenetic, and Isolation-by-Distance Analyses

A 472 nt fragment of the NS3 gene of the BvHV strains was aligned using Geneious Prime 2019.1.1 and MAFFT v7.388. A phylogenetic tree was constructed from the alignment using MrBayes v3.2.7 [35], with a Markov chain Monte Carlo algorithm, using the GTR+I+G substitution model, as determined using jModelTest v2.1.10 [33], run for 6 × 10⁶ generations; results were visualized with FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).

A test for isolation-by-distance was performed including all BvHV sequences described here. Isolation-by-distance is the result of the accumulation of mutations in viral strains in local populations and spatially limited dispersal, and manifests as a statistical association between genetic differences and geographic distance [36]. Genetic distances between pairs of partial NS3 gene sequences from the study sites were estimated as p-distance using MEGA X [37]. For the isolation-by-distance analysis, geographic distances between the trapping locations were measured with the package geosphere v1.5-10 in the R (version 4) software environment [38].