Fig. 4: Environmental conditions associated with the richness and genetic divergence of ARGs in Listeria.

a Spearman’s partial correlation between the richness of ARGs in Listeria and environmental variables, controlled for genetic similarity to L. monocytogenes. Positive and negative correlation is indicated by purple and orange, respectively. b Venn diagram of VPA showing the variation of the functional ARG richness explained by environmental variable categories with significant correlations detected (i.e., geographic locations, soil properties, and surrounding land use) and genetic similarity to L. monocytogenes. Residuals indicate unexplained variation. c MDS analysis for genomes with (orange) and without (blue) ARGs based on environmental conditions. Each dot represents a genome. PERMANOVA P = 0.001 (R² = 0.260 and pseudo-F = 6.768). Ellipse size is determined by two times the standard deviation from the mean. d Volcano plot illustrating the significance (two-sided Mann-Whitney; y-axis) of the difference in environmental variables (fold change; x-axis) compared between Listeria sensu stricto and sensu lato species. Variables above the red dashed line have an adjusted P < 0.05. Dots are color-coded by environmental variable categories. e Receiver operating characteristic (ROC) curve for the prediction of ARG presence from environmental variables using a random forest model (auROC = 0.76). Each curve reflects one evaluation using holdout data, repeated 10 times, denoted by light blue lines. The dark blue line represents the mean performance across these repetitions. f Mantel tests between the sequence dissimilarity and environmental variables for a given ARG. Positive and negative correlation is indicated by blue and yellow, respectively. g Venn diagram of VPA showing the variation of the genetic divergence of norB explained by environmental variable categories. For a and f P-values were adjusted for multiple comparisons using the Benjamini-Hochberg false discovery rate (BH-FDR) method. Significance levels are denoted by “*”, “**”, “***”, and “****” for P < 0.05, P < 0.01, P < 0.001, and P < 0.0001, respectively, and “ns” indicates not significant.