Microbe Domestication and the Identification of the Wild Genetic Stock of Wine Yeasts

Abstract

For millennia that humans have used yeasts of the genus Saccharomyces in the production of foods and beverages, unwittingly fostering their domestication. However, little is known about their ecology, distribution and natural history. This thesis aimed to investigate the geographic distribution and population structure of new wild lineages and their relationship with domesticated wine stocks in two industrially important yeasts, S. cerevisiae and its cryotolerant relative S. uvarum. Using an extended collection at a global scale of previously uncharacterised wild isolates combined with population genomic approaches, it is shown that geographic populations in S. cerevisiae and S. uvarum thrive in natural habitats and have genetic histories independent of the industrial variants. Wild lineages closely related to domesticated stocks were found in the two species. However, whereas in S. cerevisiae the domesticated wine strains form a distinct lineage from their putative wild ancestors of Mediterranean oaks, in S. uvarum wine and cider strains and their wild Holarctic relatives could not be resolved at the phylogenetic and population structure levels, indicating different routes for the transition from wild to domesticate. In both cases, introgressions and horizontally transferred regions represented major discontinuities between wine and wild strains, and are likely to denote relevant domestication fingerprints in wine yeasts of both species. In addition, wine and Mediterranean oaks strains of S. cerevisiae also showed extensive sequence divergence at non-coding sites and DNA binding proteins, which is interpreted as a by-product of domestication. The results presented here constitute a first molecular indication of domestication in S. uvarum and also highlight a more complex population history in S. cerevisiae than previously thought. Altogether, these findings provide new insights into the general mechanisms of adaptation in eukaryotic microbes and illuminate the emergence of modern industrial microbial strains from wild variants.