How genetic parasites persist despite the purge of natural selection

Genetic parasites, such as transposons, plasmids and viruses, are ubiquitous in cellular life forms. Although the selfish nature of these genetic elements is undeniable, the actual cost that they impose on their host and the mechanisms by which they counteract natural selection remain unclear. We combined mathematical models and comparative genomics to disentangle the roles of selection, horizontal gene transfer, gene duplication and gene loss in the spread and persistence of genetic parasites. By quantifying the mean contribution of transposons, conjugative plasmids, prophages and toxin-antitoxin modules to the fitness of microbial hosts, we provide evidence that these genetic elements are deleterious at evolutionary timescales. Moreover, the transfer rates experienced by selfish genetic elements exceed the minimum rates required for their long-term survival, which fully characterizes these elements as parasites.