High-throughput CRISPR-based reconstruction of mutations along evolutionary trajectories

Evolution experiments in laboratories provide ideal systems to study evolutionary processes. Our lab has conducted a long-term evolution experiment with 96 yeast populations, independently evolving for around 14,000 generations. We see populations achieve similar phenotypic values. However, the evolved genotypes of the populations are quite different. Each population has its own trajectory, with stochasticity at the sequence level caused by forces such as mutation and drift. Yet, global patterns of declining fitness adaptation over time have been seen across all populations. Epistatic interactions between acquired mutations and the genetic background are also believed to influence evolutionary trajectories. These interactions have been proposed to make mutations less beneficial in fitter backgrounds. We aim to reconstruct mutations acquired along the evolutionary trajectory, in a variety of genetic backgrounds along the course of evolution. A recently-developed CRISPR-based method allows us to engineer many desired edits across the whole genome. We aim to study the effects of frequently observed, putatively beneficial mutations as well as their distributions of fitness effects. Using distinctly evolved lines from the experiment, we seek to answer questions about how adaptive mutations constrain evolutionary trajectories and better understand the relationship between highly beneficial mutations and the epistatic interactions they have with various genetic backgrounds.