Host shifts result in parallel genetic changes when viruses evolve in closely related species

Ben Longdon; Jonathan P Day; Joel M Alves; Sophia CL Smith; Thomas M Houslay; John E McGonigle; Lucia Tagliaferri; Francis M Jiggins

We next examined whether the same genetic changes occur in parallel when different populations 82 encounter the same host species. Of the 584 SNPs, 102 had derived allele frequencies >0.05 in at 83 least two viral lineages, and some had risen to high frequencies in multiple lineages (Figure 1 ). We 84 estimated the genetic differentiation between viral lineages by calculating F ST . We found that viral 85 lineages that had evolved within the same host were genetically more similar to each other than to 86 lineages from other host species (Figure 2 ; P<0.001). Furthermore, we found no evidence of 87 differences in substitution biases in the different host species (Fisher Exact Test: p=0.14; see 88 methods), suggesting that this pattern is not driven by changes in the types of mutations in different 89 host species.