Mutational bias and local genome context constrain adaptive paths in experimental evolution

Experimental evolution provides a reproducible testing ground for the study of adaptive evolution where the numerous degrees of freedom impacting the trajectory of evolution can be limited to their most controlled form. Evolution in a continuous culture device known as the chemostat further constrains the variables that introduce stochasticity by maintaining constant selective pressure and environmental conditions. Using a multiplexed miniature chemostat setup, we generated a highly parallel set of yeast evolution experiments in glucose-, phosphate-, and sulfate-limited media conditions with a total of 95 replicates across the conditions. Whole genome sequencing of the resulting populations allowed us to analyze recurrent targets of mutation during these evolution experiments. Integrating the mutations observed here with previously generated data, we found consistent targeting of complexes and pathways, such as the SAGA complex in sulfate limitation, the sirtuin family in phosphate limitation, and the phosphorelay signal transduction system in glucose limitation. We also recurrently observed new mobilizations of Ty1 and Ty2 transposable elements, often interrupting genes that were also separately mutated by SNPs/InDels in other populations. Comparing the frequency of genes impacted by either SNPs and indels or Ty1/Ty2 elements, we find that a gene's location relative to predictors of Ty element mobilization likely impacted whether a gene was affected by either mutational modality. Overall, we identify how the biases in mutational frequency and the effect of local genome context can impact the direction of evolution and shape the path a population takes across the fitness landscape.