Universal bacterial clade dynamics dominate under predation despite altered phenotypes and mutation targets

Recent studies have revealed bacterial genome-wide evolution to be complex and dynamic even in a constant environment. The evolution is characterized by the emergence of new clades competing or temporarily coexisting as each clade continues to undergo evolutionary change. Previous studies on predator-prey dynamics tracking simple ecological and phenotypic metrics have shown predation to fundamentally alter prey evolution, often giving rise to defense evolution followed by frequency dependent selection between defended and undefended prey genotypes as well as coevolution. Moreover, these dynamics can differ between prey species depending, for example, on mutation rate and the physiological and fitness effects of the mutations available. Here we sought to consolidate these fields by examining genome-wide evolution in five bacterial prey species separately subjected to long-term evolution under ciliate predation. For all species, we found mutational signals of prey defense evolution, with phenotypic data demonstrating change in phenotypic composition for defense trait over time. Mutational targets and dynamics also differed between prey species. Intriguingly, however, overall temporal molecular dynamics across the prey species were strikingly similar to those of bacteria evolving alone, with constant emergence, competition and quasi-stable coexistence of clades. This makes molecular evolution more interesting and less predictable than we might expect based on existing coevolutionary theories.