Each separate gene alignment (ALN2_C, ALN2_PrM, ALN2_E, ALN2_NS1, ALN2_NS2A, ALN2_NS2B, ALN2_NS3, ALN2_NS4A, ALN2_NS4B and ALN2_NS5) was investigated for signs of positive selection. To that end, the dN/dS ratio for the whole gene, and for each codon in the alignment, was inferred using the M3 model [34] implemented in MrBayes, otherwise using default settings. Mixing of the MCMC chains, as well as the ESS of each estimated parameter was assessed by analyzing the resulting parameter files with Tracer. Each analysis was run until the ESS exceeded 200 for all parameters, after which the probability for the whole gene, or individual codons in the sequence, to have evolved under positive selection was analyzed with Tracer.