The dynamics of adaptation determine which mutations fix in a population, and hence how reproducible evolution will be. This is central to understanding the spectra of mutations recovered in the evolution of antibiotic resistance1, the response of pathogens to immune selection2, 3, and the dynamics of cancer progression4, 5. In laboratory evolution experiments, demonstrably beneficial mutations are found repeatedly6, 7, 8, but are often accompanied by other mutations with no obvious benefit. Here we use whole-genome whole-population sequencing to examine the dynamics of genome sequence evolution at high temporal resolution in 40 replicate Saccharomyces cerevisiae populations growing in rich medium for 1,000 generations. We find pervasive genetic hitchhiking: multiple mutations arise and move synchronously through the population as mutational ‘cohorts’. Multiple clonal cohorts are often present simultaneously, competing with each other in the same population. Our results show that patterns of sequence evolution are driven by a balance between these chance effects of hitchhiking and interference, which increase stochastic variation in evolutionary outcomes, and the deterministic action of selection on individual mutations, which favours parallel evolutionary solutions in replicate populations.
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- Supplementary Information (5.9 MB)
This file contains Supplementary Tables 2-3 (see separate file for Supplementary Table 1) and Supplementary Figures 1-3.
- Supplementary Table 1 (412 KB)
This file contains details of the 1,020 mutations identified in the 40 sequenced populations. It also contains complete descriptions of all mutations we observed in all 40 populations, and their frequency trajectories over the 1,000 generations of the experiment, as estimated by both independent pipelines (Methods).