Quantifying separation and similarity in a Saccharomyces cerevisiae metapopulation

Abstract

Eukaryotic microbes are key ecosystem drivers; however, we have little theory and few data elucidating the processes influencing their observed population patterns. Here we provide an in-depth quantitative analysis of population separation and similarity in the yeast Saccharomyces cerevisiae with the aim of providing a more detailed account of the population processes occurring in microbes. Over 10 000 individual isolates were collected from native plants, vineyards and spontaneous ferments of fruit from six major regions spanning 1000 km across New Zealand. From these, hundreds of S. cerevisiae genotypes were obtained, and using a suite of analytical methods we provide comprehensive quantitative estimates for both population structure and rates of gene flow or migration. No genetic differentiation was detected within geographic regions, even between populations inhabiting native forests and vineyards. We do, however, reveal a picture of national population structure at scales above ∼100 km with distinctive populations in the more remote Nelson and Central Otago regions primarily contributing to this. In addition, differential degrees of connectivity between regional populations are observed and correlate with the movement of fruit by the New Zealand wine industry. This suggests some anthropogenic influence on these observed population patterns.

Quantifying the relative roles of selective and neutral processes in defining eukaryotic microbial communities

“…Further, we provide evidence that there is significant distance decay between fungal communities, within at least soils, over distances of about 100 km. This overall result nicely recapitulates patterns revealed from the population genetic analyses of just one species in this community sourced from these same samples: Saccharomyces cerevisiae (Knight and Goddard, 2014). The recovery of the same patterns at both the species and community level lends confidence to the ability of these data to reveal underlying biological signals.…”

Cellar-Associated Saccharomyces cerevisiae Population Structure Revealed High-Level Diversity and Perennial Persistence at Sauternes Wine Estates

“…By sampling 21 different white and red ferments across three different regions in New Zealand, Gayevskiy and Goddard (12) obtained 353 S. cerevisiae isolates and 274 genotypes (78%) using 10 microsatellite markers, which is similar to our data but with lower diversity. However, our estimate of yeast diversity suggests that the Sauternes region is expected to contain an extremely high diversity of S. cerevisiae strains, with an underlying population of more than 72,533 unique genotype strains (with a wide confidence interval), a figure far higher than the estimate of 1,700 inferred for the New Zealand vineyard (52). The diversity index obtained for the Sauternes S. cerevisiae population was also similar to the diversity index obtained for the Merlot red wine cellar S. cerevisiae population.…”

Impact of Commercial Strain Use on Saccharomyces cerevisiae Population Structure and Dynamics in Pinot Noir Vineyards and Spontaneous Fermentations of a Canadian Winery

“…cerevisiae population structure on a global scale [27–29], geography appears to be a significant driver of structure within wine- and vineyard-associated S . cerevisiae populations as found in New Zealand [21,23,26] and Portugal [20,24]. These studies, however, have examined yeast communities in regions that range from 10km to 1000km in distance.…”