Revisiting the Taxonomic Synonyms and Populations of Saccharomyces cerevisiae – Phylogeny, Phenotypes, Ecology and Domestication

Saccharomyces cerevisia, the most emblematic and industrially relevant yeast species, has a long list of taxonomical synonyms. Formerly considered as distinct species, some of the synonyms represent variants with important industrial implications, like S. boulardii or S. diastaticus, but with an unclear status, especially among the fermentation industry, the biotechnology community and between biologists not informed on taxonomical matters. Here, we use genomics to investigate a group of 45 reference strains (type strains) of former Saccharomyces species that are currently regarded as conspecific with S. cerevisiae. We show that these variants are distributed across the phylogenetic spectrum of domesticated lineages of S. cerevisia, with emphasis on the most relevant technological groups, but totally absent in wild lineages. We analysed the phylogeny of a representative and well-balanced dataset of S. cerevisia genomes that deepened our current ecological and biogeographic assessment of wild populations and allowed the distinction between wild populations associated with low- and high-sugar natural environments. Some wild lineages from China were merged with wild lineages from other regions in Asia and in the New World, thus deepening the current model of expansion from Asia to the rest of the world. We reassessed several key domestication markers among the different domesticated populations. In some cases we could trace their origin to wild reservoirs, while in other cases gene inactivations associated with domestication were also found in wild populations, thus suggesting that natural adaptation to sugar-rich environments predated domestication.