Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

There is growing evidence that parallel molecular evolution is common, but itscauses remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism.Here we test the hypothesis that bottleneck intensity shapes parallel evolutionby elucidating the genomic basis of adaptation to antibiotic-supplementedmedium in hundreds of populations of the bacterium Pseudomonas fluorescensPF0-1. As expected, bottlenecking decreased the rate of phenotypic andmolecular adaptation. Surprisingly, bottlenecking had no impact on the likelihood of parallel adaptive molecular evolution at a genome-wide scale.However, bottlenecking had a profound impact on the genes involved in anti-biotic resistance. Specifically, under either intense or weak bottlenecking,resistance predominantly evolved by strongly beneficial mutations whichprovide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of geneticmechanisms, significantly reducing the observed levels of parallel geneticevolution. Our results demonstrate that the population bottlenecking canbe a major predictor of parallel evolution, but precisely how may be morecomplex than many simple theoretical predictions.