DOI: 10.5061/dryad.k3f17
title: Data from: Evolution of ecological dominance of yeast species in high-sugar environments

description: 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.
description: Pyrosequencing
 competition dataCalibrated
 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.csvSequencing competition dataCalibrated 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.csvHigh-sugar environmentData 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.csvEthanol resistanceData 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.csvSupernatant inhibitorsData 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.csvSequencing metadataBarcodes, indexes and metadata used to extract species tags from raw sequencing data for BITS-3 and BITS-4 libraries.Metadata.xlsBITS-3 library readRaw sequence data with reads containing barcode, linker then species specific sequences.BITS-3_S1_L001_R1_001.fastq.gzBITS-3 library indexRaw sequence data with reads containing indexes.BITS-3_S1_L001_I1_001.fastq.gzBITS-4 library readRaw sequence data with reads containing barcode, linker then species specific sequences.BITS-4_S1_L001_R1_001.fastq.gzBITS-4 library indexRaw sequence data with reads containing indexes.BITS-4_S1_L001_I1_001.fastq.gz