Competition and Coexistence in Yeast Experimental Evolution

Abstract

Natural selection gives rise to biodiversity by purging the less-fit among variants that are too similar (a principle known as character displacement), but to predict how fit or different an organism needs to be to survive is hard. In the simplest theoretical case, the probability whether one lineage versus another survives depends only on their relative fitness and random fluctuations. In more complex scenarios, this probability may depend on the fitness of all the other lineages in the population, mutations that these and other lineages acquire before the outcome of competition is decided, and additional ecological interactions. These complexities evolve readily in laboratory microbial populations, suggesting that they are the norm in Nature, and have been extensively studied theoretically. This thesis provides one of the few empirical examples in which the evolution and mechanism of some of these complexities have been characterized and modeled sufficiently to make basic predictions, such as whether a mutation will fix or go extinct, which competing lineages may or may not coexist, and how do these processes relate? This work was carried out in an established system for experimental evolution, populations of asexual budding yeast (S. cerevisiae) in microtiter plates. Chapter 2 demonstrates an experimental design and modeling approach to infer the distribution of fitness effects of beneficial mutations from the population-dynamics of genetic markers. The inferred distribution accurately predicts fixation probabilities of lineages and adaptation rates of populations. Chapter 3 describes a new example of spontaneously-evolved coexistence between types competing for the same resources, including the physical mechanism, genetic basis and a mathematical model of the coexistence. The conclusion provides additional analyses to connect the findings from these two chapters and discusses their implications for microbial evolution more generally and directions for future work.