Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae

Abstract

Saccharomyces cerevisiae is predominantly found in association with human activities, particularly the production of alcoholic beverages. S. paradoxus, the closest known relative of S. cerevisiae, is commonly found on exudates and bark of deciduous trees and in associated soils. This has lead to the idea that S. cerevisiae is a domesticated species, specialized for the fermentation of alcoholic beverages, and isolates of S. cerevisiae from other sources simply represent migrants from these fermentations. We have surveyed DNA sequence diversity at five loci in 81 strains of S. cerevisiae that were isolated from a variety of human and natural fermentations as well as sources unrelated to alcoholic beverage production, such as tree exudates and immunocompromised patients. Diversity within vineyard strains and within saké strains is low, consistent with their status as domesticated stocks. The oldest lineages and the majority of variation are found in strains from sources unrelated to wine production. We propose a model whereby two specialized breeds of S. cerevisiae have been created, one for the production of grape wine and one for the production of saké wine. We estimate that these two breeds have remained isolated from one another for thousands of years, consistent with the earliest archeological evidence for winemaking. We conclude that although there are clearly strains of S. cerevisiae specialized for the production of alcoholic beverages, these have been derived from natural populations unassociated with alcoholic beverage production, rather than the opposite. The budding yeast, Saccharomyces cerevisiae, has been used to make bread, beer, and wine for thousands of years. To investigate the evolutionary history of this species, the authors examined DNA sequence variation from a large collection of yeast strains isolated from a variety of sources, including saké wine, grape wine, clinical samples, tree exudates, and fruit. The DNA sequence diversity among these strains shows that both saké and grape wine strains form two distinct groups that have remained isolated for a substantial period of time. The data suggest that S. cerevisiae consists of both “wild” and “domesticated” populations and that at least two independent domestication events lead to extant grape wine and saké wine strains.