Fig. 4: Global phylogeny Salmonella Enteritidis from poultry.
a Maximum-likelihood phylogeny of 914 selected poultry, human, and other isolates from 46 countries. The tree is rooted at midpoint. Three major lineages (Global, Atlantic, and US) are delineated. Each isolate is color coded by the continent of origin. The isolates from humans and poultry (including chickens and eggs) are indicated. Poultry Salmonella Enteritidis clades specific to Chile, Brazil, and Mauritius are delineated. Arrowheads indicate isolates whose phage types are publicly available. ATL, Atlantic. The scale bar indicates 50 SNPs. b Circular cladogram of the same maximum-likelihood phylogeny of the 914 isolates. Colored circles indicate internal nodes that have a squared coefficient (R2) of the Spearman or Pearson correlation between isolation years and branch lengths >0.4. The sizes of the circle are proportional to the values of R2 (0.4–0.9). The Global and the Atlantic lineages that exhibit strong temporal signals of SNP accumulation are shaded in gray.
