Phylogenetic relationships of 46 Salmonella enterica subsp. enterica strains and one S. enterica subsp. arizonae isolate as inferred by ClonalFrame based on sequence data for 93 loci. Values above the branches are posterior probabilities and are only indicated when > 0.9. Horizontal bars to the right of the tree indicate mixture of ancestry as inferred by STRUCTURE, the coloration being proportional to the amount of genetic material inherited from a putative ancestral population (red and blue = clade A, green = clade B, yellow = a putative non-subspecies enterica ancestor, in this case represented by S. enterica subsp. arizonae). The blocks to the right of the mixture of ancestry indicate the distribution of the β- glucuronidase operon (green), SPI-18 (blue) and the CdtB-islet (gold) in the genomes. The CdtB-islet in S. Inverness has been marked with an asterisk because of its position on a mobile element.