In budding yeasts, fermentation in the presence of oxygen evolved around the time of a whole genome duplication (WGD) and is thought to confer dominance in high-sugar environments because ethanol is toxic to many species. While there are many fermentative yeast species, only Saccharomyces cerevisiae consistently dominates wine fermentations. In this study, we use co-culture experiments and intrinsic growth rate assays to examine the relative fitness of non-WGD and WGD yeast species across environments to assess when S. cerevisiae's ability to dominate high-sugar environments arose. We show that S. cerevisiae dominates nearly all other non-WGD and WGD species except for its sibling species S. paradoxus in both grape juice and a high-sugar rich medium. Of the species we tested, S. cerevisiae and S. paradoxus have evolved the highest ethanol tolerance and intrinsic growth rate in grape juice. However, the ability of S. cerevisiae and S. paradoxus to dominate certain species depends on the temperature and the type of high-sugar environment. Our results indicate that dominance of high-sugar environments evolved much more recently than the WGD, most likely just prior to or during the differentiation of Saccharomyces species, and that evolution of multiple traits contributes to S. cerevisiae's ability to dominate wine fermentations.
Pyrosequencing competition data
Calibrated pyrosequencing data from Competition 1. The frequency of each competitor species in either paired competition with S. cerevisiae or in pooled monocultures. The adjusted frequency is based on calibration curves and eliminates negative values.
CalibratedPyrosequencingData.csv
Sequencing competition data
Calibrated sequencing data from Competition 2. The frequency of each competitor species in competition with different reference strains, along with concatenated barcode and indexes used for sample ID. The fitness difference and experimental metadata is also included.
biodiversity.data.csv
High-sugar environment
Data from assays (gren01 and nut01) to determine the intrinsic growth rate of each yeast species in high-sugar environments including grape juice. The OD600 (cell density) is given for time-points between zero and 48 hrs.
grape_environment.csv
Ethanol resistance
Data from assay to determine the ethanol tolerance of each yeast species. OD600 (cell density) is given for time-points between zero and 48 hrs for different concentrations of ethanol. One sample was omitted from the analysis (Smik, Rep C, 2% ethanol) due to possible contamination from a pipetting error that occurred during the experiment.
ethanol.csv
Supernatant inhibitors
Data from assay to determine whether Saccharomyces cerevisiae produces unknown compounds that inhibit the growth of other yeast species. OD600 (cell density) is given for for time-points between zero and 48 hrs in supernatant cultures. A small number of samples (24/432) registered growth in un-innoculated controls before 36 hours, and these samples were omitted from our analysis. Following the removal of those samples, Lachancea kluyveri lacked sufficient control samples for analysis and was not included in the analysis.
supernatant.csv
Sequencing metadata
Barcodes, indexes and metadata used to extract species tags from raw sequencing data for BITS-3 and BITS-4 libraries.
Metadata.xls
BITS-3 library read
Raw sequence data with reads containing barcode, linker then species specific sequences.
BITS-3_S1_L001_R1_001.fastq.gz
BITS-3 library index
Raw sequence data with reads containing indexes.
BITS-3_S1_L001_I1_001.fastq.gz
BITS-4 library read
Raw sequence data with reads containing barcode, linker then species specific sequences.
BITS-4_S1_L001_R1_001.fastq.gz
BITS-4 library index
Raw sequence data with reads containing indexes.
BITS-4_S1_L001_I1_001.fastq.gz