Bayesian phylogenetic trees were constructed with a GTR+I+G nucleotide substitution model for the concatenated alignment of NS3 and a GTR+G model for the recombinant partition. Model selection was based on the corrected Akaike information criterion in MrAic [28] . For each alignment, two separate analyses were run simultaneously with MrBayes v.3.2-cvs [29] (source code accessed with CVS 22 January 2009) for 5000000 generations using the default settings for priors and MCMC proposals. Trees were sampled every 1000 th generation, and standard deviation of split frequencies was below 0.01 at the end of each analysis. For all Bayesian analyses (i.e. MrBayes and BEAST), mixing of the MCMC chains and effective sample size (ESS) for each parameter estimate were investigated using Tracer v.1.5 [30] which showed convergence and larger than 200 ESS for each summary statistic. For both MrBayes analyses, the first 2500 trees where discarded as burn-in and the 7500 remaining trees were summarized in a majority-rule consensus tree.