Map (a) and maximum clade credibility tree (b) of SCSK G gene sequences used in the study.

<p>Posterior probabilities are shown for key nodes, and timescale is present at the bottom. To show the phylogenetic position of SCSK in the context of other related RABV lineages, several representative G gene sequences of raccoon RABV (RACCOON), north-central/central Mexican skunk RABV (MXSK), bat RABV (BAT) are shown, and a canine RABV is used as an outgroup.</p

The reconstruction of spatiotemporal dynamics of SCSK inferred from the Bayesian skygrid model: dispersal rate (a) and wavefront velocity (b).

<p>Years are shown on the horizontal axis. The dashed lines indicate 95% HPD.</p

The reconstructed spatiotemporal diffusion of SCSK at different time points from 1860 to 2013.

<p>Black lines show a spatial projection of a representative phylogeny, with each node being mapped to its known (external node) or estimated (internal node) location. In each panel colored clouds (cumulative, in different colors for each state) represent statistical uncertainty in the estimated locations of the SCSK lineages (95% HPD regions). In the last panel (2013), white circles indicate isolate sampling locations.</p

Test results for positive selection analysis, and summary of amino acid substitutions.

1<p>Significance of test statistics (* <i>P</i><0.05, ** <i>P</i><0.01).</p>2<p>The infinite value is due to absence of synonymous change in foreground branch.</p>3<p>The information is arranged in the order: position, change, branch.</p>4<p>Amino acid changes with bold character were changes that occurred at terminal branches.</p

Convergent changes among branches of interest in the bat and terrestrial RABV datasets.

1<p>Branch numbers are corresponding to the number shown in the nodes (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002786#ppat.1002786.s001" target="_blank">Figure S1</a>).</p

Reconstruction of post-host shift amino acid changes.

<p>Left: Bayesian tree of EF-W1 lineage, based on the entire coding region of G gene (1572 nuc). The branches involved in host-shift are marked with red. The amino acid changes occurred within these branches were defined “post-host shift” changes. Other branches that lead to terrestrial mammal RABV are marked with green. Right: the magnification of the three clusters involved in the Flagstaff host shifts. For clarity, the branch length did not reflect substitutions per site. The branches with non-synonymous changes are marked with pink, and numbers of changes are shown above and below. For more details see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002786#ppat-1002786-t002" target="_blank">Table 2</a>.</p

Bayesian tree of the EF-W1 lineage.

<p>Skunk viruses are colored in red, fox viruses are colored in blue, other mesocarnivoran viruses are colored in green; bat viruses are black. Posterior probabilities are indicated at key nodes.</p