Rabies occupancy probability over time.

<p>Top. Occupancy probability for all sites over time (blue line, shading: 95% credible intervals) using Model 11b, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005822#pntd.0005822.t001" target="_blank">Table 1</a>). Grey bars: number of samples collected. Middle. Occupancy probability in space and time. Bottom. Coefficient of variation for occupancy probabilities over space and time. Middle and bottom: Data were aggregated over a 6-month time frame (corresponding to the X-axis labels of the top row plot). Black triangles represent city locations (Fort Collins, Greeley, Boulder and Longmont); sizes scaled to the human population size of the cities. Topographical divide from <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005822#pntd.0005822.g001" target="_blank">Fig 1</a>, which indicates land above 1829 m (6000 feet), is indicated by the black line.</p

Map of study area.

<p>Each dot represents the location where a dead skunk was reported and subsequently tested for rabies. Grid cells show the scale at which the study area was gridded (8 x 8 km sites, i = 1, …, M).</p

Model selection and fit statistics for within- and out-of-sample predictions.

<p>Model selection and fit statistics for within- and out-of-sample predictions.</p

Phylogeographic inference of viral spatial dynamics.

<p>A) Spatio-temporal projection of the maximum clade credibility tree from the phylogeographic analysis. Transparent polygons indicate the 80% HPD of infected area through time. Grey shading on the left indicates landscape that is above 1829 m. Grey lines indicate major highways. Blue lines indicate all waterways, including very minor and ephemeral ones. Stars indicate the centers of major cities (as in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005822#pntd.0005822.g001" target="_blank">Fig 1</a>). B) Spatial expansion of RABV in skunks, displayed as the distance from the inferred epizootic origin in the phylogeographic analysis. Grey shading indicates the HPD₉₅. The solid black line is the median distance. C) The distance traversed by each branch in the phylogenetic tree divided by the expected number of infections along that branch, assuming a generation time of 30 days. The histogram shows distances calculated from the 144 branches of 500 randomly-selected trees from the posterior distribution of the phylogeographic analysis. Grey bars are the inner HPD₉₅.</p

Parameter estimates from the best predictive model of occupancy probability (Model 11b, Table 1) and the phylogeographic model.

<p>Parameter estimates from the best predictive model of occupancy probability (Model 11b, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005822#pntd.0005822.t001" target="_blank">Table 1</a>) and the phylogeographic model.</p

Rates of spatial spread.

<p>Model 11b was used to predict spatial spread of rabies. Points are the predicted distance in km of new colonizations from the southern-most grid-cell row. Size of the points corresponds to numbers of new colonizations at a given distance from the southern-most row. The slope (red line) gives a monthly rate of southerly spread (21.1 km/yr). Shaded area gives the 95% confidence intervals of the slope. The 6-month intervals shown on the X-axis correspond to those in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005822#pntd.0005822.g004" target="_blank">Fig 4</a>.</p

Current geographic distribution of rabies virus variants in the continental US and Canada.

<p>Current geographic distribution of rabies virus variants in the continental US and Canada.</p

Summary of modeling approaches used to understand rabies dynamics in wildlife, conceptually structured as in Keeling and Rohani [90].

<p>Summary of modeling approaches used to understand rabies dynamics in wildlife, conceptually structured as in Keeling and Rohani [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005249#pntd.0005249.ref090" target="_blank">90</a>].</p

Previously published ORV campaigns in North America and the estimated population seroprevalence in response to vaccination.

<p>Previously published ORV campaigns in North America and the estimated population seroprevalence in response to vaccination.</p

Different within- and between-host mechanisms are hypothesized to produce different evolutionary patterns of viral diversity at the level of populations and individuals.

<p>Different shapes represent different viral strains within a population and different colors within a shape reflect variation within strains that have a recent common ancestor. (A) In the case of SIR/SIRS dynamics, acute infections are reintroduced and then cleared at the population level between each pulse. At each point in time, the pathogen within individuals in the population either has the same genotype (e.g., blue circles at pulse 1, red squares at pulse 2) or has closely related genotypes with a common ancestor (matching shape but different color). (B) In the case of SILI dynamics, individuals remain infected over time. Genetic diversity is determined in part by within-host viral evolution. Therefore, genotypes are likely to differ among individuals (many unique shape and color combinations, with some consistency over time). (C, D) Illustrative phylogenies of the virus populations across pulses. (C) In a scenario of viral extinction and reintroduction, all strains at a given pulse are closely related and have a recent common ancestor. (D) Divergent strains (different symbols) may be detectable within pulses, and distinctive strains are maintained across pulses. The hexagon and pentagon represent unsampled viral diversity present in the population.</p