Extended Data Fig. 5: Lineage assignment with PopPunk.

PopPunk was used to divide each species into sequence clusters (SCs). For each species, the number of components to fit in the mixture model (k) was chosen based on the scatter plot of core and accessory distances. The model was then fit, and the boundary refined using an iterative process of moving the boundary and reassessing the network features. In all cases the core boundary was used to define the clusters. The number of isolates, number of SCs, model K, and core distance boundaries are shown for each species.