Ale yeasts: probably the oldest microbial pets known to mankind
Taken together, these findings shed light on how the combination of life history and niche adaptation shaped the genome of S. cerevisiae ale yeasts. It becomes increasingly clear that today's industrial S. cerevisiae yeasts are genetically and phenotypically separated from wild stocks due to human selection and trafficking. Maybe even more interesting is that the thousands of industrial yeasts that are available today seem to stem from only a few ancestral strains that made their way into food fermentations and subsequently evolved into separate lineages, each used for specific industrial applications. Within each cluster, strains are sometimes further subdivided along geographical boundaries, as is the case for the Beer 1 clade (Gallone et al., 2016), which is divided into three main subgroups.
However, it is important to note that strains from different fermentation environments experienced fundamentally different evolutionary paths. Continuous growth in man-made, rich beer medium led to large changes in the genome (e.g. aneuploidies, major chromosomal rearrangements) and the loss of survival skills outside this specialized niche. This is in sharp contrast to wine yeasts, for example, which experience the grape must environment only for a short period during the year and persist the rest of the time in and around vineyards or in gut of insects. Therefore, wine strains are exposed more often to natural, nutrient-poor environments, and consequently have characteristics that are more similar to the strains encountered in the wild. Moreover, these frequent ‘back to nature' events probably induce sporulation (sexual reproduction) and thus favour hybridization with wild yeasts. In addition, the different common practices for wine and brewing industries have a strong influence on the effective population size of yeast populations and as a consequence, on the patterns of molecular evolution and variation. Because beer is produced throughout the year and beer yeasts are recycled for a few batches of fermentation each time, trillions of cells are transferred when a new batch is inoculated. By contrast, for wine yeasts only a relatively small amount of cells will contribute to the next harvest season grape must. This has resulted in a high genetic diversity within beer yeasts compared to the more uniform wine yeast population. Together, this makes ale strains the most domesticated S. cerevisiae strains around, and explains why they are such a perfect fit for beer fermentations. However, this also implies that these yeasts fail to perform well in more innovative brewing conditions (e.g. very high gravity brewing), as they encounter new stresses for which they are usually not adapted, while other strains from different lineages often are.