On the inferred network (Figure 2 ), the region of the split-graph separating the four main clusters exhibits a significant ''tree-like'' structure that rules out frequent recombination between the clusters. Nevertheless, a prominent split associated with SSEV (DQ235152) and LIV (Y07863) indicates a marked conflicting and/or ambiguous signal that could be associated with a recombination event. This hypothesis was first examined with RDP3, wherein all methods identified the LIV strain as displaying signs of homologous recombination between the SSEV strain as the major parent and a strain belonging to W-TBEV as the minor parent ( Figures S1 a-b) . All methods recognized with significance that an insert within the NS3 gene of LIV originated from a W-TBEV strain, but they were not consistent with respect to the precise location of the two recombination methods. When run simultaneously, all methods bar, Chimaera and MaxChi, identified Neudoerfl (U27495) as the minor parent and estimated the breaking points at nt 5787 and 5991. When the data were analyzed with Chimaera or MaxChi as single primary detection methods, they instead proposed, with significance (P-value ,3.10 22 ), slightly different breakpoints (Table 1) .