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Mutations that occurred during L. plantarum experimental evolution in mice. A Pie chart reporting the number of Lp genes that accumulated mutations over the course of each experimental evolution setup (Host- and Diet-exclusive mutations) and in both setups (shared). B Total summed frequencies of all mutations observed in each sample from the mouse host evolution experiment. The panel above shows the structure of the evolution experiment in mouse hosts. Bacterial populations were sequenced at the indicated time points. C Base substitution spectra observed in the mouse diet, as well as mouse host populations divided into all mutations and those associated with the mutS A41T and mutS Δ1303 mutator lineages (see Additional file 5: Fig. S5). D Frequency trajectories of the mutS A41T and mutS Δ1303 mutations and mutations in other DNA replication and repair genes (mutL, dinB, dnaE) that may alter mutation rates in the mouse host populations

Mutations occurred during L. plantarum experimental evolution in the fly setup. A Pie chart reporting the number of Lp genes that accumulated mutations over the course of each experimental evolution setup (Host- and Diet-exclusive mutations) and in both setups (Shared). B Total summed frequencies of all mutations observed in each sample from the Host and Diet evolution experiment. Each point represents the mean of the 3 experimental replicates analyzed, with bars indicating the standard deviation (SD). C Base substitution spectra observed in the fly host and diet. The total number of mutations detected in each group (N) is shown above each bar. D Dynamics of mutations in fly diet and host treatments. Muller plots representing the evolutionary dynamics of Lp genes that mutated in the Host and Diet-evolved populations across EE cycles 2, 8, 14, and 20 (i.e., after 176, 704, 1232, and 1760 Lp generations) 2b1af7f3a8