To investigate any potential spatial genetic structure among isolates within each species, we computed pairwise Nei’s genetic distances matrices [38], between each isolate within each species (i.e. S. haematobium = all 11 nominal S. haematobium isolates + the Corsican hybrid isolate; and S. bovis = the six nominal S. bovis isolates), based on the initial filtered 56,181 SNPs and using the dartR package [39]. Correlation between the resulting matrices of pairwise Nei’s distances and pairwise geographical distances computed between the geographical origin of each isolate were next tested within each species using two independent Mantel tests as implemented in the ‘ape’ package [40] in R. Significance of correlations were assessed by comparing the obtained Z-scores to 10,000 Z-values generated after bootstrapping. Because uncertainty existed concerning the precise sampling location for some isolates, we considered the centroid of each country of origin obtained from QGIS v. 2.8.12 (QGIS Development Team).

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