Several methods were used to extract recombination signal from ALN1 with the RDP3beta36 package [20] , because inspection of the split network had established the possibility of recombination within the species (see results). All analyses were carried out with Bonferroni correction (P-value,0.05) and signals reported by more than one method were retained. RDP [21] , GENECONV [22] , BootScan [23] , MaxChi [24] , Chimaera [20] , and SiScan [25] were used for screenings the alignment. For this initial phase, the following settings were modified to balance sensitivity and statistical significance: RDP: window size 25, detect recombination between sequences sharing 90% to 100% identity; GENECONV: G-scale 5; BootScan: windows size 100, use NJ trees, 200 bootstrap replicates, cutoff percentage at 95% and Jin and Nei 1990 model; Chimaera: 40 variable sites per window; SisScan: window size 80, slow exhaustive scan. As all methods detected the presence of significant recombinant signals in the NS3 gene, the dataset was further evaluated for phylogenetic evidence of recombination based on an alignment of NS3-sequences derived from ALN1.