Endosymbiont evolution: predictions from theory and surprises from genomes

Genome data have created new opportunities to untangle evolutionary processes shaping microbial variation. Among bacteria, long‐term mutualists of insects represent the smallest and (typically) most AT‐rich genomes. Evolutionary theory provides a context to predict how an endosymbiotic lifestyle may alter fundamental evolutionary processes—mutation, selection, genetic drift, and recombination—and thus contribute to extreme genomic outcomes. These predictions can then be explored by comparing evolutionary rates, genome size and stability, and base compositional biases across endosymbiotic and free‐living bacteria. Recent surprises from such comparisons include genome reduction among uncultured, free‐living species. Some studies suggest that selection generally drives this streamlining, while drift drives genome reduction in endosymbionts; however, this remains an hypothesis requiring additional data. Unexpected evidence of selection acting on endosymbiont GC content hints that even weak selection may be effective in some long‐term mutualists. Moving forward, intraspecific analysis offers a promising approach to distinguish underlying mechanisms, by testing the null hypothesis of neutrality and by quantifying mutational spectra. Such analyses may clarify whether endosymbionts and free‐living bacteria occupy distinct evolutionary trajectories or, alternatively, represent varied outcomes of similar underlying forces.