Comparison of typical trees derived from ER-like networks (top row) and NATSAL networks (middle row) illustrating that pathogen prevalence (bottom row) as well as networks both influence trees.

<p>The NATSAL trees displays early divergence compared to the ER trees, and this affects the number of clusters. Panel A shows different epidemic trajectories and their corresponding trees, B shows more similar trajectories, and C shows closely matched epidemics. The tree differences are most modest in panel C where the pathogen population dynamics are closely matched. Edges in each cluster are drawn with the same colour. The threshold value for clustering was 0.1.