The frequency of SNPs in viral lineages that have evolved in different host species.

<p>Each row represents an independent viral lineage. Viruses that evolved in different host species are separated by black horizontal lines. Each column represents a polymorphic site in the DCV genome, and only sites where the derived allele frequency >0.05 in at least two lineages are shown. The intensity of shading represents the derived allele frequency. Sites where there are three alleles have the two derived allele frequencies pooled for illustrative purposes. Sites with SNP frequencies that are significantly correlated among lineages from the same host species are shown by red stars at the bottom the column (permutation test; <i>p</i><0.05). Open reading frames (ORFs) and viral proteins based on predicted polyprotein cleavage sites [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006951#ppat.1006951.ref038" target="_blank">38</a>–<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006951#ppat.1006951.ref042" target="_blank">42</a>] are below the x axis. Information on the distribution of mutations across the genome and whether they are synonymous or non-synonymous can be found in the supplementary results. Sites with missing data are shown in white. The phylogeny was inferred under a relaxed molecular clock [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006951#ppat.1006951.ref033" target="_blank">33</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006951#ppat.1006951.ref043" target="_blank">43</a>] and the scale axis represents the approximate age since divergence in millions of years (my) based on estimates from: [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006951#ppat.1006951.ref035" target="_blank">35</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006951#ppat.1006951.ref036" target="_blank">36</a>].