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. 2025 Mar 4;13:RP101241. doi: 10.7554/eLife.101241

Figure 2. Phylogenetic tree of S. Gallinarum L2b and L3b based on a spatiotemporal Bayesian framework.

The phylogenetic tree on the left was constructed using a reference-mapped multiple core-genome SNPs sequence alignment, with recombination regions detected and removed by Gubbins. The spatiotemporal Bayesian framework was configured with the ‘GTR’ substitution model, 4 Gamma Category Count, ‘Relaxed Clock Log Normal’ model, ‘Coalescent Bayesian Skyline’ tree prior model, and a Markov Chain Monte Carlo (MCMC) chain length of 100,000,000, with sampling every 10,000 iterations. Convergence was assessed using Tracer, ensuring all parameter effective sampling sizes (ESS) exceeded 200. Evolutionary time is represented by the length of the branches. The heatmap on the right displays, respectively, the sequence type (ST), region of isolation, and the number (Num.) of antimicrobial resistance genes (ARGs) carried by the corresponding Salmonella Gallinarum. (a) indicates the phylogenetic tree for Lineage 2b, (b) indicates the phylogenetic tree for Lineage 3b.

Figure 2.

Figure 2—figure supplement 1. Phylogenetic tree of Salmonella Gallinarum L1 based on a spatiotemporal Bayesian framework.

Figure 2—figure supplement 1.

The phylogenetic tree on the left was constructed using a reference-mapped multiple core-genome SNPs sequence alignment, with recombination regions detected and removed by Gubbins. The spatiotemporal Bayesian framework was configured with the ‘GTR’ substitution model, 4 Gamma Category Count, ‘Relaxed Clock Log Normal’ model, ‘Coalescent Bayesian Skyline’ tree prior model, and a Markov Chain Monte Carlo (MCMC) chain length of 100,000,000, with sampling every 10,000 iterations. Convergence was assessed using Tracer, ensuring all parameter effective sampling sizes (ESS) exceeded 200. Evolutionary time is represented by the length of the branches. The heatmap on the right displays, respectively, the sequence type (ST), region of isolation, and the number (Num.) of antimicrobial resistance genes (ARGs) carried by the corresponding Salmonella Gallinarum.
Figure 2—figure supplement 2. Phylogenetic tree of Salmonella Gallinarum L2a based on a spatiotemporal Bayesian framework.

Figure 2—figure supplement 2.

The phylogenetic tree on the left was constructed using a reference-mapped multiple core-genome SNPs sequence alignment, with recombination regions detected and removed by Gubbins. The spatiotemporal Bayesian framework was configured with the ‘GTR’ substitution model, 4 Gamma Category Count, ‘Relaxed Clock Log Normal’ model, ‘Coalescent Bayesian Skyline’ tree prior model, and a Markov Chain Monte Carlo (MCMC) chain length of 100,000,000, with sampling every 10,000 iterations. Convergence was assessed using Tracer, ensuring all parameter effective sampling sizes (ESS) exceeded 200. Evolutionary time is represented by the length of the branches. The heatmap on the right displays, respectively, the sequence type (ST), region of isolation, and the number (Num.) of antimicrobial resistance genes (ARGs) carried by the corresponding Salmonella Gallinarum.
Figure 2—figure supplement 3. Phylogenetic tree of Salmonella Gallinarum L3c based on a spatiotemporal Bayesian framework.

Figure 2—figure supplement 3.

The phylogenetic tree on the left was constructed using a reference-mapped multiple core-genome SNPs sequence alignment, with recombination regions detected and removed by Gubbins. The spatiotemporal Bayesian framework was configured with the ‘GTR’ substitution model, 4 Gamma Category Count, ‘Relaxed Clock Log Normal’ model, ‘Coalescent Bayesian Skyline’ tree prior model, and a Markov Chain Monte Carlo (MCMC) chain length of 100,000,000, with sampling every 10,000 iterations. Convergence was assessed using Tracer, ensuring all parameter effective sampling sizes (ESS) exceeded 200. Evolutionary time is represented by the length of the branches. The heatmap on the right displays, respectively, the sequence type (ST), region of isolation, and the number (Num.) of antimicrobial resistance genes (ARGs) carried by the corresponding Salmonella Gallinarum.
Figure 2—figure supplement 4. Assessment of the temporal structure (L1-L3c).

Figure 2—figure supplement 4.

The plots depict the root-to-tip regression analysis for the Salmonella maximum likelihood tree, generated using TreeTime software. Each data point on the plot represents a measurement from the root to each tip in the tree, with the solid line indicating the regression line.
Figure 2—figure supplement 5. Historical international transmissions of S. Gallinarum biovar Pullorum (bvSP) lineages L2b and L3b are depicted with arrows representing the transmission paths. The pink and red lines represent L2b and L3b, respectively.

Figure 2—figure supplement 5.

Figure 2—figure supplement 6. Recombination removal using Gubbins.

Figure 2—figure supplement 6.

Recombination in five lineages (L1, L2a, L2b, L3b, L3c) were removed using Gubbins with default parameters. The recombination regions for each lineage were mapped onto the reference genome, S. Gallinarum R51. Different colors represent the number of recombination events in each S. Gallinarum lineages strains, with darker colors indicating higher frequencies of recombination.