The Role of Protein-coding and Regulatory Evolution in Speciation of Wild Yeast

The evolutionary processes leading to the generation of new species has been studied extensively in plants and animals; however, due to the challenges of studying microbes, microbial speciation has received less attention. This project aims to thoroughly characterize a case of eukaryotic microbial speciation on the genetic level, specifically, the effects of migration and divergence on the wild yeast, Saccharomyces paradoxus. Previous studies have shown there are two isolated populations— one in North America, and one in Europe— and a third migrant population that originally came from Eurasia but is currently inhabiting North America. The migrant population has been genetically diverging since its arrival and now avoids mating with the North American population, suggesting an on-going speciation process. This research used publically available genomic data, as well as data collected in our lab, to quantify genetic differences between the three populations. I investigated all of the protein- coding genes in the wild yeast genome to determine the effects of migration and adaptation to a new environment. The results showed that the European and migrant populations are undergoing the very beginning of speciation. One nuclear gene, PET111, which encodes a mitochondrial regulatory protein, appears to have been under significant positive selection, indicating the possibility of mito-nuclear coevolution. The importance of adaptive mutations in protein-coding vs. regulatory regions of the genome has been a hotly-debated topic in evolutionary developmental biology (“evo devo”). To address this controversial question, for each gene in the genome, I quantified neutral genetic divergence within the gene and compared it to the nucleotide diversity of the adjacent cis- regulatory regions. Confirming the “evo-devo” tenet, the results showed that more changes are accumulating in the cis-regulatory regions than in the protein-coding regions under neutral, and that the regulatory variation may be under selection in the diverging migrant population