Figure 5

Phylogeny of generalist and specialist Campylobacter lineages. (A) Phylogenetic tree and isolation source of 74 common C. jejuni and C. coli sequence types (STs). The tree was constructed from a concatenated gene-by-gene alignment of 595 core genes, using ClonalFrameML with the standard model where recombination parameters are shared by all branches using the transition/transversion parameter estimated by PhyML. The heatmap represents the number of hosts in which particular STs were isolated, based on analysis of 30239 pubMLST isolate records. The scale bar represents the number of substitutions per site; (B) Quantification of the variation in number of hosts from which each ST has been sampled for all lineages shown in the tree, highlighting a gradient between host specialism and generalism; (C) Comparison of clustering on the tree, calculated as the estimated number of SNP corresponding to the average branch tip distance to the last common ancestor (LCA) with the number of hosts of isolation of each examined ST. There is no correlation between the two datasets (linear regression; r² = 0.037).