Developing the wine yeast Lachancea thermotolerans as a model for evolutionary genomics.

How do species adapt to their environments? This question has been a major driver ofevolutionary genetics research for a century. Developing cost-efficient models to address how traits are shaped by their environments and how species adapt to distinct ecological niches is critical as the impact of human influence on the environment becomes clearer. This dissertation develops the use of the wine yeast Lachancea thermotolerans as a model for population genomics by investigating the phylogenetics, population history, and phenotypic variation within the species. Firstly, I summarized population structure using over 300 genome sequences from strains with a broad range of geographic and environmental origins. Expansion of available genomic resources to include 90 more isolates from European and North American woodland habitats across two continents revealed several new tree-associated lineages. Additionally, I found evidence for recent gene flow between continents, providing a more complete view of population structure and the impact of environment on genetic variation. The addition of wild strains suggested that copy number variation previously associated with adaptation to domestic environments may be more prevalent across ecological and geographical origins than previously thought. Secondly, analysis of growth rates at a range of temperatures showed natural genetic variation within L. thermotolerans. Strains from one North American lineage grew at a significantly lower rate than others at high temperatures. This suggests a single change within the species that appears maladaptive at high temperatures has occurred. The lack of adaptation seems surprising because there was natural genetic variation in growth rates among L. thermotolerans strains, suggesting that standing variation exists for adaptation to high temperature growth. Population genomic analyses require high-quality data to determine differences within a species, and the data used here did not show intraspecies contamination. This is important because, using simulated data, I found that contamination between 5 and 10% can alter phylogenetic tree topology and gene flow. Overall, the results presented here emphasize the importance of screening for intra-species contamination prior to phylogenetic or population genomic work and demonstrate the potential of L. thermotolerans as a model system to increase understanding of the genetic mechanisms of adaptation.