Phylogenies of CCapSV, DImmSV and PAegRV

Phylogenies of CCapSV, DImmSV and PAegRV were inferred in MrBayes (v3.2.5). A general time reversible model with gamma distributed rate variation and a proportion of invariable sites was used, with parameters estimated from the data during the analysis.  A site-specific rate model was used, that allowed each codon position to have its own rate. Models were run for 1 million MCMC generations, with trees being sampled every 1000 generations. The first 25 per cent of the trees were discarded to ensure that the chains had reached stationarity, and a consensus tree was created from the remaining trees. Trees are midpoint rooted.