From lab to lager: An investigation of adaptation, admixture, and ale brewing yeasts

Abstract

Creating a predictive model of evolution is a central goal of biology and necessitates understanding the genetic basis of adaptation. Using experimental evolution, adaptation can be explored in real time and connected to genetic variation through sampling and sequencing a population over several generations. I use a general paradigm of evolving and resequencing to explore the genetic basis of adaptation from the laboratory to the brewery. First, I explore population sequencing data from a set of over a hundred evolution experiments conducted in continuous culture devices under glucose-, phosphate- and sulfur-limitation and find a high level of reproducibility of evolutionary outcomes. Specifically, by correlating the frequencies of mutational outcomes with datasets indicating the frequency and relative fitness of the mutations, I find that genome context likely influences the outcomes of adaptive evolution. Next, I explore the effect of environment, specifically temperature on the adaptation and evolution of a proto-lager hybrid that resembles the ancient hybridization between S. cerevisiae and S. eubayanus. Through experimental evolution in conditions favoring either of the two parental species, I find that, at certain loci, the parental genome is retained in conditions favorable to that species, indicating that environment has an effect on hybrid genome evolution. Finally, I explore the evolution of beer brewing yeasts within the natural niche of the brewery through partnerships with breweries across North America. By sequencing serially reused populations of beer yeast and phenotyping clonal isolates from the populations, I find that structural variation in the form of mitotic recombination and aneuploidy likely contribute to the adaptation and domestication of the beer brewing yeasts. Overall, findings across all three systems support the notion that the results of adaptive evolution are highly reproducible and that non-stereotypical forms of variation such as mitotic recombination and copy number variation play a vital role in evolution.