Fig. 2

E. rectale consists of four geographically stratified subspecies. a Maximum likelihood phylogenetic tree of all E. rectale genomes, built from a concatenated core gene alignment using PhyloPhlAn2 (“Materials and methods”) and rooted based on a phylogenetic tree including E. rectale sister species. b Non-metric multidimensional scaling plot of pairwise genetic distances between all E. rectale genomes. c Distribution of intra- and inter-subspecies core gene genetic distances. p values were obtained using bidirectional Wilcoxon rank-sum tests. d Subspecies assignment using PAM clustering with k = 4 (“Materials and methods”). Black points indicate genomes obtained from cultured isolate sequencing