Fig. 2: Phylogeographic reconstruction and spatiotemporal ancestry of a virus collected in Switzerland (EPI_ISL_413021).

a Phylogenetic cluster with the Swiss virus shaded in gray in the MCC tree, and the same B.1 cluster with branches colored according to posterior modal location states inferred by an analysis using sampling location only. The tip for the Swiss virus corresponding to the trajectory in b is indicated with an arrow. Markov jump trajectory plot depicting the ancestral transition history between locations from Hubei up the sampling location for the Swiss genome, using b sampling location only, c travel origin location, and d sampling location and travel history. The trajectories are summarized from a posterior tree distribution with Markov jump history annotation. A horizontal line in a trajectory represents the time during which a particular location state is maintained in the spatiotemporal ancestry of the virus. An example of such an ancestry is highlighted in gray in the MCC tree cluster. A vertical line represents a Markov jump between two locations in the trajectory. The most prominent locations in the posterior trajectories are ordered along the Y-axis together with “other”, which represents all remaining locations. The relative density of lines reflects the posterior uncertainty in location state and transition time between states.