title: Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution.
abstract: There is growing evidence that parallel molecular evolution is common, but its causes 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 evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular 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 antibiotic resistance. Specifically, under either intense or weak bottlenecking, resistance predominantly evolved by strongly beneficial mutations which provide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of genetic mechanisms, significantly reducing the observed levels of parallel genetic evolution. Our results demonstrate that population bottlenecking can be a major predictor of parallel evolution, but precisely how may be more complex than many simple theoretical predictions.
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK t.vogwill@imperial.ac.uk.
authors.forename: Tom
authors.identifier: 0000-0003-1044-6623
authors.initials: T
authors.lastname: Vogwill
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
authors.forename: Robyn L
authors.initials: RL
authors.lastname: Phillips
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
authors.forename: Danna R
authors.initials: DR
authors.lastname: Gifford
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK craig.maclean@zoo.ox.ac.uk.
authors.forename: R Craig
authors.initials: RC
authors.lastname: MacLean
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D004352:Drug Resistance, Microbial / Q000235:genetics*; D019143:Evolution, Molecular; D009154:Mutation; D010641:Phenotype; D011551:Pseudomonas fluorescens / Q000235:genetics*
keywords: evolutionary rescue; experimental evolution; genome sequencing; parallel evolution; population bottlenecks