(A) Ratio of clones from each coevolving population that are susceptible (green), non-capsulated (light pink), capsulated lysogens (beige), or capsulated but resistant by other undefined mechanisms (dark pink). N.B. Dashed line indicates when the x-axis, no longer follows a linear scale. Dark arrows indicate the time points from which the lysogens tested in panel C were retrieved. (B) Growth of newly lysogenized clones reveals significant death during the exponential phase (in the absence of induction), as measured by the optical density. Black line corresponds to the control, BJ1 ancestor. (C) PFU/mL produced without induction by five selected new lysogens derived from BJ1 and isolated at day one for A4 and A6 (Population #2, MMC), at day four for B3 (Population #3, MMC), and day nine for H8 and H9 (Population #3, MMC). Dashed line indicates the limit of detection of the essay. Each black dot represents an independent biological replicate (independent strain lysate) and large red dots represent the mean. Error bars correspond to the standard deviation. Two-sided t-test ‘a’, p<0.001 compared to ancestor BJ1 (negative control, C-) and ‘b’, p<0.05 compared to ST14 (phage producer, positive control, C+). (D) Simulated temporal dynamics of the proportion of lysogens in the populations, as calculated by eVIVALDI. Each circle corresponds to the central tendency of replicate simulations, with the different colors indicating a given probability of spontaneous prophage induction (shown in the legend, values approximated to the nearest major integer). The error bars correspond to the standard deviation across the replicate simulations. In the represented simulations, the probability of acquisition of a phage resistance mutation (capsule loss) is 0.001, and the fitness cost of this mutation is 10% of the bacterial growth rate, as calculated in Buffet et al., 2021.