Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

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Abstract
Gavin Sherlock and colleagues report an experimental genome evolution study in Saccharomyces cerevisiae demonstrating adaptive evolution by clonal interference. The classical model of adaptive evolution in an asexual population postulates that each adaptive clone is derived from the one preceding it1. However, experimental evidence has suggested more complex dynamics2,3,4,5, with theory predicting the fixation probability of a beneficial mutation as dependent on the mutation rate, population size and the mutation's selection coefficient6. Clonal interference has been demonstrated in viruses7 and bacteria8 but not in a eukaryote, and a detailed molecular characterization is lacking. Here we use three different fluorescent markers to visualize the dynamics of asexually evolving yeast populations. For each adaptive clone within one of our evolving populations, we identified the underlying mutations, monitored their population frequencies and used microarrays to characterize changes in the transcriptome. These results represent the most detailed molecular characterization of experimental evolution to date and provide direct experimental evidence supporting both the clonal interference and the multiple mutation models.