Phylogenetic tree of S . Typhimurium genomes. Maximum likelihood tree for S. Typhimurium based on SNPs identified by mapping to the reference chromosome for S. Typhimurium SL1344 (isolate details in Tables 1 and 2), excluding those SNPs identified in phage or repeat regions. Inset shows a neighbour-joining split network of the same SNP data. Shaded region indicates S. Typhimurium 135@ isolates sequenced in this study, for which a high resolution tree is given in Figure 2; red branches indicate the farm clone. Bootstrap support is shown for those bipartitions with <100% bootstrap support; tree branches are labelled with the number of SNPs contributing to the branch.