Phage clone phylogenies for four simulations with different cross-reactivities: no cross-reactivity (A), exponential cross-reactivity with (B), and step-function cross-reactivity with (C) and (D). All simulations share all other parameters: . Phage clones are plotted at the first time they pass a population size of 2 to remove clutter from many new mutations destined for extinction, and the size of each circle is logarithmically proportional to the maximum size reached by that clone. Colours indicate the time of extinction of each clone. For each simulation with cross-reactivity, the left inset shows phage (top) and bacteria (bottom) clone sizes over time; colours indicate unique clone identities. Coloured rectangles above insets in (C) and (D) correspond to the dominant clone at each time. Dominant clone identities are offset by (vertical dashed line for visual aid).