Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages

Fig. 1.. Linear regression of sample collection dates against divergence from the root of reconstructed maximum-likelihood trees from FMDV VP1 sequences. Circles representing tip nodes are colored according to the corresponding FMDV lineage. Fitted lines are shown with their estimated 95% confidence interval regions. R-squared (R2) and slope (β) parameters estimated for each fitted regression line are reported.

Fig. 2.. Space-time phylodynamics of FMDV lineages circulating in Western and Southern Asia between 1997 and 2018. In the left panel, combined maximum clade credibility (MCC) tree reconstructed for each of the FMDV lineages investigated. Branches and nodes are colored according to the most probable ancestral location inferred from the discrete phylogeography analysis. (a) Evolution of the weighted dispersal velocity (y-axis, expressed in km/year) through time (x-axis) estimated using continuous phylogeography methods and reconstructed for each of the FMDV lineages. (b) Inferred FMDV lineage ancestry makeup (y-axis) through time (x-axis) estimated from the combined MCC tree topologies. (c) Proportion of ancestral locations of FMDV lineages (y-axis) through time (x-axis) extracted from the combined phylogenetic tree trunks as inferred from the discrete phylogeographic analysis. The plots were reconstructed using the data used from this study, and they do not reflect FMDV lineages that were circulating and sampled prior to 2001.

Fig. 3.. Spatial dynamics of FMDV dispersal within Western and Southern Asia. (a) Size and directionality (expressed from the thin to the thick end) of discrete phylogeographic reconstructed migrations of FMDV lineages between countries (expressed by their centroids) are represented with Bezier curves, with their size proportional to the median number of Markov jumps inferred from the discrete phylogeographic analysis and summed across all three FMDV lineages. (b) Continuous phylogeographic diffusion in space and time showing the 95% highest posterior density (HPD) contours (kernel density estimates) computed for each FMDV lineages and sequentially colored by year with gradients ranging from light (time of the most recent common ancestor) to dark (time of the most recent sample). The HPD regions were derived from 100 trees uniformly sampled from the posterior space of the continuous phylogeographic model results.

Fig. 4.. Ancestral evolution and genetic diversity of FMDV sublineages circulating in Western and Southern Asia. (a) Horizontal lines represent the evolutionary duration of each FMDV sublineage from the time of the first to the time of the last sampled isolate (the individual dot for PanAsia-2KAT-15 denotes a single report). Ancestral links between FMDV sublineages are represented by arches, with their starting point denoting the time of the most recent common ancestor (tMRCA). The area of circles is indicative of the number of sequences present for each FMDV sublineage. (b) Between- (β) and within- (α) sublineage diversity is expressed using the Rao’s quadratic entropy, with the size of the circle proportional to the estimated entropy value. Estimates of α-diversity are represented by circles present in the diagonal of the correlogram.

Fig. 5.. Dynamics of FMDV lineages in host species within Western and Southern Asia. (a) Posterior distribution of evolutionary persistence of FMDV lineages in different host species obtained from the structured coalescent analysis. Evolutionary persistence is expressed as a measure of the waiting time (in years) for a datum FMDV lineage to be transmitted between different host species. (b) Kernel density estimates of FMDV lineages dispersal within single host species superimposed to the population density of host species distribution (expressed in heads/km2) defined within the boundaries of Western, Central, and Southern Asia. The 95% highest posterior density (HPD) regions were derived from 100 trees uniformly sampled from the posterior space of the structured coalescent analysis and aggregated to the continuous phylogeographic model results. The spatial raster of population density for each host species was sourced from the FAO Gridded Livestock of the World (Gilbert et al. 2018).