Figure 1.
Phylogenetic tree containing results of the discrete state model.
Maximum clade credibility phylogeny for YFV under the discrete state transition model. Legend color indicates highest probability state transition for annotated node.
Table 1.
Divergence estimates for major lineages.
Figure 2.
Bayesian skyline demographic analysis for the prM/E alignment.
Plot is a trace of the effective population size over time of the YFV alignment, using a Bayesian skyline model. Mean population size (black line) is displayed with upper and lower bounds of the 95% HPD interval (blue and purple lines). Constant value of the trace between years 1940 and 2010 is indicative of stability in the estimated viral population during that time.
Figure 3.
Map of supported state transitions for Bayesian Stochastic Search Variable Test (BSSVS).
Colored lines represent the transitions that were statistically supported in the inferred phylogeny, using an uncorrected model. Significance was assessed for state transitions resulting in a Bayes factor greater than 5 and BSSVS indicator value greater than .50.
Table 2.
Bayes factors for state transitions, comparing significance output for uncorrected vs. distance-penalized connections.
Figure 4.
Map of the African continent containing projection of the tree and uncertainty for Cauchy-distributed random walk diffusion.
The inferred phylogeny is projected along a time gradient, with mean root location and results of the diffusion analysis. Colored polygon surfaces represent 80% HPD uncertainty for the location of estimated nodes, using Cauchy-distributed diffusion rates for ten equal time intervals along the length of the tree. Polygons are overlaid with a maximum entropy raster considering the presence of Aedes africanus on the African continent.