Figure 1.

Inferred relative time of insertion of putative horizontally acquired genes, using Typhi CT18 as the query genome. The reference tree topology, based on whole-genome sequence alignment, is shown in the upper section of the figure, with the pseudo-code describing the algorithm for inferring the relative time of insertion shown at the bottom. Node 1 predates the Bongori-Arizonae-Enterica lineage. Node 2 predates the Arizonae-Enterica lineage. Node 3 predates the S. enterica lineage. Nodes descendant of node 3 are inferred relative to the query genome: node 4_[TS] (Typhoidal Salmonella) predates the Typhi-Paratyphi A lineage, and node 4_[NTS] (non-Typhoidal Salmonella) predates the Typhimurium-Enteritidis-Gallinarum lineage. Node 5_[STY] (STY: S. typhi) predates the CT18-TY2 lineage, node 5_[SPA] (SPA: S. paratyphi A) predates the SARB42 - AKU_12601 lineage, and node 5_[STM] (STM: S. typhimurium) predates the SL1344-DT104-LT2 lineage. (Note on node 6, relative to LT2: for a fully resolved tree, that is, with fully bifurcating topologies, polytomies, for example, trichotomies, are not allowed. Although Typhimurium LT2 and DT104 are assigned in the same node (node 6), with SL1344 in an apparently separate branch under node 5_[STM], the three Typhimurium strains are very close phylogenetically; moreover, there are no genes restricted on branch 6, that is, genes shared between LT2 and DT104 that are absent from SL1344. For these reasons, throughout this analysis, node 6, relative to LT2, is ignored and node 5_[STM] is considered to be the Typhimurium lineage-specific node.)