Understanding the mechanism of diversity generation through directional selection

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PROJECT SUMMARY Understanding the general rules of adaptation has implications for treating diseases caused by evolving entities such as cancer and drug-resistant infections. In attempts to uncover these general rules, previous research has revealed a seemingly paradoxical phenomenon. On the one hand, under selective pressure, adaptive mutations arise quickly, have large fitness effects, localize to a few functionally similar genes, and likely exploit the same adaptive strategy. On the other hand, laboratory-evolved organisms show a wide range of diverse physiological changes. This means that directional selection increases rather than decreases phenotypic diversity. This phenomenon likely explains our limited ability to predict the effectiveness of anticancer therapies, because even genetically similar cancers can have highly diverse physiologies. In this project, I will use a collection of several hundred well-studied adaptive S. cerevisiae mutants, isolated from a single evolution experiment, to test two mechanistic hypotheses of how selection might generate diversity. My working hypothesis is that selection generates diversity through combinatorial loss of plastic responses. The alternative hypothesis is that selection generates diversity through the gain of novel responses. To distinguish between these two hypotheses, I will measure the molecular phenotypes of the adaptive mutants with two RNA sequencing technologies. In Aim 1, I will use bulk RNA sequencing on 10 carefully selected mutants, grown in the environment in which they evolved, in order to gain the first insight into the molecular mechanism of their adaptive strategy. In Aim 2, I will use a state-of-the-art, high-throughput, barcode-aware RNA sequencing approach called Split-Seq to measure the full scope of the adaptive mutants' phenotypes which are most prominent in various extreme environments. This will reveal if the adaptive mutants achieve high fitness in the evolution environment and high diversity in other environments through loss of plasticity or by creating novel responses. Uncovering the mechanism of how selection generates diversity will contribute to our general understanding of adaptation and have implications for treating diseases driven by evolutionary adaptation, such as cancer and drug-resistant infections. During my PhD, I received strong training in molecular genetics and learned basic wet lab skills but had little exposure to evolutionary theory or genomics. Undertaking this project will greatly expand my conceptual and technological toolkit, as I will learn molecular evolution and population genetics, as well as genomics methods like barcode tracking and RNA sequencing. I will receive formal and informal training in evolutionary theory, programming, genomics data analysis, grant writing, and professional leadership. This will prepare me to become an independent researcher and leader in the interdisciplinary field of molecular and evolutionary biology.