Supplementary Information.

<p><b>Fig A.</b> Example dynamics from different regions of parameter space shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g001" target="_blank">Fig 1</a>. Numerical simulations of a continuous flow model using the following parameters: <i>α</i> = 0.5 h<sup>-1</sup>, uncompensated plasmid-bearer relative fitness = 0.82, compensated plasmid relative fitness = 0.95, <i>K</i> = 5.7 × 10<sup>9</sup> ml<sup>-1</sup>, <i>μ</i> = 0.04125. The base conjugation rate <i>γ</i> was set above the “domination” threshold at 9.9 × 10<sup>−12</sup> ml.cells<sup>-1</sup>h<sup>-1</sup> and was reduced below <i>γ</i><sub><i>dom</i></sub> or the “invasion” threshold for compensated and uncompensated plasmids-bearers to explore parameter space. The compensated plasmid conjugation rate <i>γ</i><sub><i>C</i></sub> = <i>γ</i><sub><i>Q</i></sub> was set at for cases where <i>γ</i><sub><i>C</i></sub> = <i>γ</i><sub><i>Q</i></sub>><i>γ</i><sub><i>dom</i></sub>, at where <i>γ</i><sub><i>inv</i></sub> < <i>γ</i><sub><i>Q</i></sub> = <i>γ</i><sub><i>C</i></sub><<i>γ</i><sub><i>dom</i></sub>, and at for cases where <i>γ</i><sub><i>Q</i></sub> = <i>γ</i><sub><i>C</i></sub><<i>γ</i><sub><i>inv</i></sub>. The uncompensated plasmid conjugation <i>γ</i><sub><i>P</i></sub> rate was set at for <i>γ</i><sub><i>inv</i></sub><<i>γ</i><sub><i>P</i></sub><<i>γ</i><sub><i>dom</i></sub> and at where <i>γ</i><sub><i>P</i></sub><<i>γ</i><sub><i>inv</i></sub>. Details on parameterisation are provided in Table A in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.s001" target="_blank">S1 File</a>. (A) Examples across parameter space for chrCM with initial density at 0.01 <i>K</i>, initial plasmid carriage at frequency of 50%, with 50% of these with CM. Coloured bars below each subpanel header indicate the corresponding regions of parameter space highlighted in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g001" target="_blank">Fig 1</a>. (B) As (A) but for plaCM. (C) Different initial conditions for (the pink region of <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g001" target="_blank">Fig 1A</a>). In both cases, plasmid-bearers start at 50% of the total, but in the left hand-panel the CM is at 50% of this population, whereas on the right it is 0.01%. The boundary for the initial conditions, solved analytically, is provided in Supplementary Text B in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.s001" target="_blank">S1 File</a>, and the data underlying this figure can be found in <a href="https://dx.doi.org/10.5281/zenodo.13963497" target="_blank">https://dx.doi.org/10.5281/zenodo.13963497</a>. <b>Fig B.</b> Approximate Extended Simonsen conjugation rates for pQBR57 and pQBR57::plaCM. The dotted line indicates the previously measured conjugation rate for wild-type pQBR57 [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.ref012" target="_blank">12</a>]. The data underlying this figure can be found in <a href="https://dx.doi.org/10.5281/zenodo.13963497" target="_blank">https://dx.doi.org/10.5281/zenodo.13963497</a>. <b>Fig C.</b> Individual replicates for the summarized data presented in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g003" target="_blank">Fig 3</a>. Red/Yellow and Yellow/Red refer to the orientation of the fluorescent markers (chrCM / plaCM), and Yes / No refers to mercury selection. The data underlying this figure can be found in <a href="https://dx.doi.org/10.5281/zenodo.13963497" target="_blank">https://dx.doi.org/10.5281/zenodo.13963497</a>. <b>Fig D.</b> Individual replicates for the summarized data presented in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g004" target="_blank">Fig 4</a>. Red/Yellow and Yellow/Red refer to the orientation of the fluorescent markers (chrCM / plaCM), and Yes / No refers to mercury selection. The data underlying this figure can be found in <a href="https://dx.doi.org/10.5281/zenodo.13963497" target="_blank">https://dx.doi.org/10.5281/zenodo.13963497</a>. <b>Fig E.</b> Individual replicates for the summarised data presented in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g005" target="_blank">Fig 5</a>. The data underlying this figure can be found in <a href="https://dx.doi.org/10.5281/zenodo.13963497" target="_blank">https://dx.doi.org/10.5281/zenodo.13963497</a>. <b>Fig F.</b> Individual replicates for the summarised data presented in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g006" target="_blank">Fig 6</a>. The data underlying this figure can be found in <a href="https://dx.doi.org/10.5281/zenodo.13963497" target="_blank">https://dx.doi.org/10.5281/zenodo.13963497</a>. <b>Fig G.</b> (A) ODE-based model simulations resemble plaCM versus chrCM experimental results in main text Figs <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g003" target="_blank">3</a>, <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g005" target="_blank">5</a>, and 6. Numerical simulations of a continuous flow model based on the following parameters: <i>α</i> = 0.54 h<sup>-1</sup>, SBW25::chrCM(pQBR57) relative fitness = 0.97, SBW25(pQBR57::plaCM) relative fitness = 0.95, <i>K</i> = 5.7 × 10<sup>9</sup> ml<sup>-1</sup>, chrCM conjugation rate <i>γ</i><sub><i>C</i></sub> = 4.6 × 10<sup>−12</sup> ml.cells<sup>-1</sup>h<sup>-1</sup>, plaCM conjugation rate (see main text and Fig I in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.s001" target="_blank">S1 File</a> for discussion). Details on parameterisation are provided in Table A in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.s001" target="_blank">S1 File</a>. (B) Plasmid weaponisation can drive outcomes. As panel A, except chrCM conjugation rate <i>γ</i><sub><i>C</i></sub> was set to zero. The qualitatively different outcomes between panels A and B demonstrate the role that costly plasmid transmission from compensated strains can play. An interactive version of this figure is provided by following the link at <a href="http://www.jpjhall.net/plasmid-dynamics-model" target="_blank">www.jpjhall.net/plasmid-dynamics-model</a>. The code underlying this figure can be found in <a href="https://dx.doi.org/10.5281/zenodo.13963497" target="_blank">https://dx.doi.org/10.5281/zenodo.13963497</a>. <b>Fig H.</b> Individual replicates for the summarised data presented in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.g007" target="_blank">Fig 7</a>. The data underlying this figure can be found in <a href="https://dx.doi.org/10.5281/zenodo.13963497" target="_blank">https://dx.doi.org/10.5281/zenodo.13963497</a>. <b>Fig I.</b> ODE-based model simulations resemble experimental results for low ratios. Numerical simulations of a continuous flow model based on the following parameters: <i>α</i> = 0.54 h<sup>-1</sup>, SBW25(pQBR57) relative fitness = 0.82, SBW25(pQBR57::plaCM) relative fitness = 0.95, <i>K</i> = 5.7 × 10<sup>9</sup> ml<sup>-1</sup>, uncompensated conjugation rate <i>γ</i><sub><i>P</i></sub> = 4.6 × 10<sup>−12</sup> ml.cells<sup>-1</sup>h<sup>-1</sup>, plaCM conjugation rate . Top panels indicate short-term dynamics, bottom panels longer-term dynamics. Details on parameterisation are provided in Table A in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3002926#pbio.3002926.s001" target="_blank">S1 File</a>. An interactive version of this figure is provided by following the link at <a href="http://www.jpjhall.net/plasmid-dynamics-model" target="_blank">www.jpjhall.net/plasmid-dynamics-model</a>. The code underlying this figure can be found in <a href="https://dx.doi.org/10.5281/zenodo.13963497" target="_blank">https://dx.doi.org/10.5281/zenodo.13963497</a>. <b>Fig J.</b> An excess of recipients does not favour wild-type pQBR57. Conjugation experiments were established with a 10