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.
|Number of pages||8|
|Journal||Proceedings of the Royal Society of London. B, Biological Sciences|
|Early online date||27 Jul 2016|
|Publication status||Published - 27 Jul 2016|
Bibliographical noteData accessibility. Experimental data has been deposited into Dryad (doi:10.5061/dryad.640j4). Sequences have been deposited into the European Nucleotide Archive with the study reference PRJEB14763, available at the URL: http://www.ebi.ac.uk/ena/data/view/PRJEB14763.
Funding. The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 281591 and from the Royal Society.
- experimental evolution
- population bottlenecks
- evolutionary rescue
- genome sequencing
- parallel evolution
- BENEFICIAL MUTATIONS
- CONVERGENT EVOLUTION
- PARALLEL EVOLUTION
- POSITIVE SELECTION
- FITNESS LANDSCAPES
- SEQUENCING DATA