Intracellular competition shapes plasmid population dynamics

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.