DOI: 10.5061/dryad.05qfttffx
title: Intracellular competition shapes plasmid population dynamics

description: Conflicts between levels of biological organization are central to
 evolution, from populations of multicellular organisms to selfish genetic
 elements. Plasmids—extrachromosomal, self-replicating genetic elements
 that face selective pressures on their hosts, but also compete within the
 cell for replication—are an ideal system for studying multilevel
 selection. While theory indicates that within-cell selection matters for
 plasmid evolution, experimental measurement of these dynamics has remained
 elusive. Here we measure the within-cell fitness of competing plasmids and
 characterize drift and selective dynamics. We achieve this by the
 controlled splitting of synthetic plasmid dimers, creating balanced
 competition experiments. We find that incompatible plasmids co-occur for
 longer than expected due to methylation-based plasmid eclipsing. Moreover,
 low-transcription plasmids display a within-cell advantage over their
 competition and fix preferentially. Critically, fixation depends
 non-trivially on gene dominance. Taken together, our results show that
 plasmid evolution is driven by dynamics at two levels, with a
 transient—but critical—contribution of within-cell fitness.
description: # Intracellular competition shapes plasmid population dynamics Dataset
 DOI: [10.5061/dryad.05qfttffx](10.5061/dryad.05qfttffx) ## Description of
 the data and file structure These files contain macroscopic images used to
 investigate within- and between-cell plasmid fitness components ### Files
 and variables #### File: data.zip **General description:** Each folder
 contains macroscopic photos of petri dishes with bacterial colonies
 relative to the described experiments. Each Petri dish was photographed in
 three different channels: brightfield, red fluorescence, and green
 fluorescence. Each file name consists of a prefix that uniquely identifies
 a petri dish, followed by a channel identifier ("BF" for
 brightfield, "mCher" for red fluorescence, and "GFP"
 for green fluorescence), and finally the file extension ".jpg".
 For instance, the photo named 20230407_153731_AC5_BF.jpg refers to the
 brightfield photo of the Petri dish identified by the string
 "20230407_153731_AC5_". Note that, for analyses, only
 fluorescence images were used, but brightfield images are provided so that
 users know what the samples looked like to the naked eye. Additionally,
 the string that identifies each Petri is composed of two parts, a
 numerical code that serves only to distinguish different replicates, and a
 alphanumerical code that carries information on the conditions of the
 experiment. These alphanumerical codes are specific to each of the
 folders. Additional information is given below for each folder.
 **ProC.Scar_ProC.Water:** This folder contains photos of growth
 experiments in which dimers were composed of quasi-neutral plasmids
 carrying the same promoter ProC. The code CC indicates that expression of
 mScarlet-I is under ProC and the expression of mWatermelon is under ProC.
 **ProA.Scar_ProC.Water:** This folder contains photos of growth
 experiments in which dimers were composed of plasmids carrying either the
 strong promoter ProC or the weak promoter ProA. The code AC indicates that
 expression of mScarlet-I is under ProA and the expression of mWatermelon
 is under ProC. **homoplasmic_cell_mix:** This folder contains photos of
 growth experiments where the innocullum was a mix of cells carrying a
 single monomeric plasmid type. Once again, the code CC indicates that
 expression of mScarlet-I is under ProC and the expression of mWatermelon
 is under ProC. **DfrA_dimers:** This folder contains photos of growth
 experiments with cells carrying dimers composed of a plasmid encoding
 mScarlet-I under the weak promoter ProA, and another plasmid encoding
 mWatermelon plus dfrA under the strong promoter ProC. Additionally dfrA
 could be under a strong or a weak RBS. file names describe the
 concentration of trimethoprim used as well as the strength of the RBS
 ("RBS30" for weak and "RBS1000" for strong).
 **DAM_neg_dfrA_dimers:** Same as the above but only for strong RBS, In
 this folder, all plasmids had the methylation sites knocked out from their
 origins. **invasion:** This folder contains photos of growth experiments
 in which cells initially contained a resident plasmid but also a
 chromosomally integrated plasmid that was released upon induction. As in
 the previous folder, file names carry information on the Trimethoprim
 concentration. Additionally, now plasmids can either be the resident
 plasmid (indicated by "pls") or the chromosomally integrated
 plasmid (indicated by "chr"). Here, the watermelon+dfrA plasmids
 are identified by the numbers "30" for the weak RBS and
 "1000" for the strong RBS. The plasmid encoding mScarlet-I under
 the weak promoter ProA was denoted by AScar. For example, the Petri dish
 identified by the string "20240214_223547_TMP0_chrAScar_pls30_"
 had no added trimethoprim ("TMP0"), had a chromosomally
 integrated plasmid encoding mScarlet-I under a weak promoter proA
 ("chrAScar"), and a resident plasmid encoding dfrA under a weak
 RBS ("pls30").  ## Code/software Images can be viewed in any
 standard image viewer