Darwinian individuality of extrachromosomal genetic elements calls for population genetics tinkering

Plasmids are extrachromosomal genetic elements commonly found in prokaryotic (and sometime eukaryotic) cells. Small plasmids are often considered cryptic and their effect on the host is elusive, while large plasmids may encode functions that are essential for the host lifestyle and attain a secondary chromosome status. Plasmids are thus an important source of raw material for microbial genome evolution outside the mainstream of bacterial chromosomes. The discovery of plasmid-mediated antibiotic resistance led to extensive research on the contribution of plasmids to the environmental dimensions of antibiotic resistance and the evolution of plasmid-host interactions following the acquisition of plasmids encoding for antibiotic resistance. Recent experimental studies revealed the importance of intracellular plasmid diversity for plasmid-host interactions. Here we describe the evolutionary forces at play during plasmid evolution in a top-down approach: this includes the effect of processes at the level of the host population and the consideration of plasmids as Darwinian individuals within the host cell.