Fig. 5

a Phylogenetic tree inferred by maximum likelihood method using the core genome SNPs of 90 S. enterica isolates. Tree is rooted by midpoint. Bootstrap values > 70% are presented on the tree. S. Dublin is indicated by green, S. Newport by blue, and S. Typhimurium by red. b Proportion of core genes with different phylogenetic clustering patterns. Genes showing a phylogenetic clustering by serotype on the tree are indicated in orange. Genes showing phylogenetic clustering of only one serotype (i.e., isolates of one serotype were grouping together while those of other two were not) are indicated in grey. Genes showing no particular clustering pattern are indicated in yellow. Conserved genes (i.e., all sequences were identical) are indicated in blue