Viral lineages from the same host species were genetically more similar to each other than to lineages from different host species.

<p>The mean pairwise <i>F</i>_<i>ST</i> between all possible pairs of viral lineages from the same host species was calculated. The red line shows the observed value. The grey bars are the null distribution of this statistic obtained by permuting the viral lineages across host species 1000 times.</p

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>].</p

Phylogenies of wild and domestic rabbits based on chord genetic distance.

<p>Trees were constructed using all 45 microsatellites. Branches are coloured according to individual’s origin. (A) Neighbour-joining tree for 471 individuals rooted with wild rabbits from the Iberian Peninsula. (B) Unrooted Neighbour-joining tree for 340 domestic individuals from 16 different breeds.</p

Reduction of genetic diversity along the rabbit domestication route.

<p>Each of the 45 circles represents a single microsatellite coloured according to the proportion of the expected heterozygosity per microsatellite present on its respective population. Note that the two wild samples (Iberian Peninsula and France) are proxies for the ancient wild samples that were involved in colonization of France and domestication. Shaded areas indicate the different bottleneck events that occurred at the colonization of France, initial domestication event, and breed formation. Values aside arrows show the amount of genetic diversity lost in each event estimated using a resampling methodology (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144687#sec002" target="_blank">Methods</a>).</p