Inferring evolutionary pathways and directed genotype networks of foodborne pathogens
Fig 8
Inference of an evolutionary step used in constructing edges in the directed genotype network.
For every genetic distance G, we use Bayesian inference to determine two temporal intervals that indicate potential evolutionary precedence. These intervals capture parent nodes that were isolated either before a child node (pre-windows) or after a child node (post-windows). The arcs in the top subfigures are cumulative probability distributions (CDFs) of these intervals for different genetic distances (number of loci modified) G. For a given level of (multiple comparisons corrected) statistical significance and genetic distance, the suitable pre- and post-windows are obtained by inverting the CDF; shown as dashed blue and red lines. Given first detection of a potential offspring MLVA profile, all nodes which are present during these intervals generate a directed edge to the offspring. The bottom subfigure illustrates inference of the four edges of the third case study, where the first three evolutionary steps crossed genetic distances of G = 1, with the final step crossing two loci (G = 2). Shaded blue and red triangles show the corresponding temporal intervals (i.e., combined pre- and post-windows) for G = 1 (blue) and G = 2 (red), in relation to the observational data points marked by vertical solid lines.