Extended Data Fig. 6: Analysis of the specificity of the types of mutations for each experimental condition during evolution.

The average similarity (in percentage) among all replicate population pairs both within groups (circular arrows) and between groups (straight arrows) for each experimental condition and each species is shown. Briefly, we analyzed the specificity of the different types of mutations (classified in NJs: Non-IS mediated, Other IS or IS1 mediated; and in SNPs: intergenic, synonymous or non-synonymous) for each condition separately for each species as described in ref. ⁴⁶. Significant differences between groups are indicated (***: p < 0.05). Based on these values, we performed two-sided permutation tests to study the significance of the specificity of mutations associated with both pOXA-48 presence (No pOXA-48 vs pOXA-48) and AMC presence (pOXA-48 vs pOXA-48 + AMC) considering all replicate populations of each species. Our results show that in none of the species the presence of AMC affected the types of mutations reported during the EE (E. coli, p = 0.124; K. pneumoniae, p = 0.231; C. freundii, p = 0.914), whereas the presence of the plasmid pOXA-48 produced significant differences in mutation types both in K. pneumoniae (p = 0.003) and C. freundii (p = 0.008), but not in E. coli (p = 0.952). The average similarity in the types of mutations was significantly lower in K. pneumoniae and C.freundii when comparing pOXA-48 carrying populations vs pOXA-48 free populations. Overall, these results support the idea that the mutation profiles were dependent on pOXA-48 presence, but not on AMC presence, in K. pneumoniae and C. freundii.