A shift from pleiotropic to modular adaptation revealed by a high-resolution two-step adaptive walk

While theoretical work suggests that adaptation should proceed by small adaptive steps which improve a small number of traits, adaptive mutations identified in microbial evolution experiments, cancer, and other systems often provide substantial fitness gains to the organisms and improve multiple traits at once. We asked whether these mutations, which often occur early in evolution and target signaling pathways, are common and observed frequently throughout adaptation or instead a rare feature of signaling pathways targeted early in adaptation. To do so, we conducted barcoded second-step evolution experiments initiated from five first-step mutations identified from an initial yeast evolution experiment. We then isolated hundreds of second-step mutations from these evolution experiments, measured their fitness and performance in several growth phases, and conducted whole-genome sequencing of the second-step clones. We find that while the vast majority of mutants isolated from the first-step of evolution in this condition show patterns of pleiotropic adaptation - improving both performance in fermentation and respiration growth phases - second-step mutations show a shift towards modular adaptation, mostly improving respiration performance and only rarely improving fermentation performance. Our results suggest pleiotropic adaptation may be common during the early stages of adaptation to a given environment, and once these become exhausted, organisms then acquire smaller, more modular mutations. Moreover, we identify a shift in the molecular basis of adaptation which suggests that genes in cellular signaling pathways may be particularly capable of providing large, adaptively pleiotropic benefits to the organism due to their ability to coherently affect many phenotypes at once.