Neighbor-joining (RapidNJ) tree of core genome allelic distances in the EcoRPlus Collection of 9479 genomes. EcoRPlus includes the draft genome with the greatest N50 value from each of the 9479 rSTs among 52,876 genomes of Escherichia within EnteroBase (August 2018) (http://enterobase.warwick.ac.uk/a/15931). The nodes in this tree are color coded by HC1100 clusters, as indicated in the key at the bottom left. Common HC1100 clusters (plus the corresponding ST Complexes) are indicated at the circumference of the tree. These are largely congruent, except that HC1100_13 corresponds to ST10 Complex plus ST168 Complex, and other discrepancies exist among the smaller, unlabeled populations. See Supplemental Figures S7, S8, respectively, for color coding by ST Complex and Clermont typing. An interactive version in which the nodes can be freely color coded by all available metadata is available at http://enterobase.warwick.ac.uk/a/15981. A maximum-likelihood tree based on SNP differences can be found in Supplemental Figure S9.
