Statistical analyses were performed with R version 3.3.2 for one-tailed Fisher’s exact test and Barnard’s test in the coinfection experiments comparing the number of sheep infected by the wt or evolved strains. For the comparison of the evolutionary dynamics of the within-host and transmitted isolates, linear models were fitted and analysis of covariance (ANCOVA) tests were performed on the mutation rates and intercepts of regression lines using type of isolates as covariate.

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