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A genomic overview of the population structure of Salmonella

Fig 3

Grapetree [31] representation of a maximum-likelihood phylogeny of core SNPs from 926 representative genomes of S. enterica plus S. bongori.

The dataset includes one representative genome from each reBG in S. enterica subspecies enterica and one representative genome from each rST in the other subspecies and S. bongori. Branches less than 0.001 substitutions per site were collapsed for clarity, whereas the branch to S. bongori (dotted line) was arbitrarily shortened to 0.4. Nodes at the tips of branches were coloured by subspecies/species, as indicated in the key. The tree indicates the likely existence of at least three genetically distinct, novel subspecies, labelled novel subsp. A through novel subsp. C. Scale bar at 02:00 in substitutions per site. A full list of strains containing the inferred species and subspecies according to this figure is available at https://enterobase.warwick.ac.uk/species/senterica/search_strains?query=workspace:9641.

Fig 3

doi: https://doi.org/10.1371/journal.pgen.1007261.g003