Figure 2.

Detailed epidemiology of three S. equi outbreaks in the United Kingdom. Isolates highlighted on the phylogeny were collected from three stables experiencing strangles outbreaks, as indicated by the key. In each case, isolates did not fall into single clades on the phylogeny; instead they were grouped into outbreak (O) and persistent (P) clusters. The positions of the outlier branches identified by root-to-tip analysis are labeled in blowups of the relevant clades. For the Essex outbreak, the number of SNPs within and between clades is indicated by the numbers in the gray boxes. Colored branches in the tree correspond to those in Figure 1.