Graphical representation of models of transmission and evolution.

<p>In the present work we consider three different models of pathogen evolution within an outbreak: <b>A)</b> The multispecies coalescent model with transmission bottlenecks, used for simulations, <b>B)</b> The structured coalescent (SCOTTI) model used for inference, <b>C)</b> The Outbreaker model also used for inference. The pictures highlight some key parameters and features of the models. Different hosts (H1, H2, H3, and H4) are represented as black rectangles. The top and bottom edge of each rectangle are the introduction and removal times of the respective hosts in <b>A</b> and <b>B</b>. The hosts with a dashed border are non-sampled. Red dots represent samples (only one per host allowed by Outbreaker), red vertical lines are lineages of the phylogeny. Smaller black dots represent coalescent events. Red arrows are transmissions/migrations in <b>B</b> and <b>C</b>. Blue tubes are transmissions with bottlenecks in <b>A</b>, and transmitted lineages are contained within them. In <b>A</b>, a transmission bottleneck from host H1 to H2 causes two lineages in H2 to coalesce (find a common ancestor backwards in time) at the same time of transmission. This does not happen at the transmission from H3 to H4, where the two lineages in H4 do not coalesce (incomplete bottleneck) and are both inherited from H3 to H4 at a single transmission event.