DOI: 10.5061/dryad.dv41ns2c5
title: Data from: Strength of selection potentiates distinct adaptive responses in an evolution experiment with outcrossing yeast

description: Selection intensity is expected to influence the magnitude and genetic
 architecture of adaptive responses, yet it is rarely evaluated as a
 standalone variable in experimental evolution studies. Here, we evolved
 outcrossing populations of Saccharomyces cerevisiae for ~200 generations
 across a spectrum of environmental stress from zero to moderate to high
 ethanol exposure, to examine how genomic responses vary with stress
 intensity. Across treatments, adaptation proceeded through many subtle
 allele and haplotype frequency shifts rather than large changes at single
 loci, consistent with a highly polygenic response. At loci associated with
 ethanol adaptation, the high stress treatment led to larger allele
 frequency changes compared to the moderate or no ethanol stress
 treatments, with the genomic architecture of adaptation becoming
 increasingly polygenic as selection intensity decreased. Moderate and high
 stress conditions engaged partially distinct biological pathways,
 indicating that selection intensity shapes both the magnitude and targets
 of adaptive change. Within this stress continuum, we also observed
 substantial, ongoing adaptation in control populations despite extensive
 prior domestication. Many alleles associated with this adaptation showed
 reduced or absent responses under ethanol stress, consistent with
 antagonistic pleiotropy. Consequently, laboratory adaptation can represent
 a major component of evolutionary change and may confound
 treatment-specific inferences when not explicitly accounted for. Broadly,
 our results demonstrate that selection intensity structures adaptive
 responses in experimental evolution and that continued laboratory
 adaptation remains an important force in these studies. Our findings
 underscore the importance of clearly defined controls and careful
 consideration of selection intensity when interpreting or comparing across
 experimental evolution studies.
description: Data is from an evolution experiment with outcrossing yeast
 populations derived from the "S12" base population, which
 originated from 12 haploid founder strains. Sixty replicate populations
 were established: 20 control (C), 20 moderate ethanol stress (M, 6%
 ethanol), and 20 high ethanol stress (H, 10% ethanol). Populations
 underwent weekly outcrossing and batch culture for 15 cycles,
 corresponding to approximately 200 generations. Growth rate assays were
 conducted at the end of the experiment to quantify adaptation by measuring
 optical density over 48 hours in control and treatment-specific media. DNA
 was extracted from pooled populations at three timepoints (cycles 1, 7,
 and 15) and sequenced using Illumina PE150. Raw reads were aligned to the
 <em>S. cerevisiae</em> S288C reference genome, and SNPs were
 called using GATK. Variant tables were filtered to retain high-confidence
 polymorphic sites. Candidate SNPs responding to selection were identified
 using a modified Cochran-Mantel-Haenszel (CMH) test, and selection
 coefficients were estimated genome-wide using Bait-ER. Haplotype
 frequencies were estimated with a sliding-window haplotype caller to
 assess the contributions of rare and founder-specific variants. More
 specific details on population maintenance, phenotyping, and sequencing
 can be found in the manuscript entitled “Increased time sampling in an
 evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae
 reveals multiple paths of adaptive change”. These datasets include growth
 measurements, SNP tables, CMH results, selection coefficient estimates,
 and haplotype frequency data for ancestral and evolved populations across
 treatments and timepoints (see ReadMe file for details). 
description: # Data from: Strength of selection potentiates distinct adaptive responses
 in an evolution experiment with outcrossing yeast ## Authors Mark A.
 Phillips, Megan Sandoval-Powers, Rupinderjit K. Briar, Marcus Scaffo,
 Shenghao Zhou, Molly K. Burke ## Corresponding Authors **Mark A.
 Phillips** (corresponding author) Email:
 [philmark@oregonstate.edu](mailto:philmark@oregonstate.edu) **Megan
 Sandoval-Powers** (co-corresponding author) Email:
 [sandovme@oregonstate.edu](mailto:sandovme@oregonstate.edu) **Molly K.
 Burke** (co-corresponding authors) Email:
 [molly.burke@oregonstate.edu](mailto:molly.burke@oregonstate.edu) ##
 Description This dataset contains data associated with the manuscript:
 Strength of selection potentiates distinct adaptive responses in an
 evolution experiment with outcrossing yeast The data are organized into
 subfolders by analysis category and contain major input and results files
 used to support the analyses and generate figures presented in the
 manuscript. These resources are intended to be used in conjunction with
 analysis scripts available on GitHub (see below). ## File Structure The
 Dryad repository consists of a single compressed (zipped) folder titled
 Phillips_2025_Yeast_Eth_dataset.zip with the following structure: ```
 Phillips_2025_Yeast_Eth_dataset/ ├── Growth_Rate_Analysis/ │ ├──
 Eth_48_hr_timepoint_0.txt │ ├── High_ethanol_2021.txt │ ├──
 Moderate_ethanol_2021.txt │ ├── Plain_ypd_2021.txt ├── Haplotype_Analysis/
 │ ├── Founders_12.txt │ ├── Input_hapcaller_ethanol.txt ├──
 Selection_Coefficient_Analysis/ │ ├── Control_BaitER_results.txt │ ├──
 High_BaitER_results.txt │ ├── Moderate_BaitER_results.txt ├──
 Candidate_SNP_Identification/ │ ├── CMH_Results_Controls_1v15.txt │ ├──
 CMH_Results_High_1v15.txt │ ├── CMH_Results_Moderate_1v15.txt ├──
 SNP_Tables/ │ ├── SNPtable_50X_scaled.txt │ ├── SNPtable_raw.txt ``` ##
 Folder and File Descriptions ### Growth_Rate_Analysis This folder contains
 input growth rate data from experimental yeast populations. Data files
 include: * `Eth_48_hr_timepoint_0.txt` — data from a plate reader assay
 measuring growth in the ancestral population across all media types for 48
 hours. * `Plain_ypd_2021.txt` — data from a plate reader assay measuring
 growth in the ancestral population and experimental populations during
 cycle 15 in plain YPD. * `Moderate_ypd_2021.txt` — data from a plate
 reader assay measuring growth in the ancestral population and experimental
 populations during cycle 15 in 6% ethanol YPD. * `High_ypd_2021.txt` —
 data from a plate reader assay measuring growth in the ancestral
 population and experimental populations during cycle 15 in 10% ethanol
 YPD. Columns generally include: * Column 1: Time in which OD600 absorbance
 was measured in minutes (time) * Column 2: OD600 absorbance measurements
 for blank media wells (blank) * Columns 3-**: OD600 absorbance
 measurements for experimental and/or ancestral populations at each
 timepoint. ### Haplotype_Analysis This folder contains input files used to
 estimate and analyze haplotype frequencies. * `Founders_12.txt` - lists
 the 12 founder haplotypes used in the experiment, with each line
 containing the full haplotype identifier name in the first column, and a
 short label in the second column. * `input_hapcaller_ethanol.txt` - major
 input file for haplotype analysis. Contains coverage and allele
 frequencies of alternative haplotypes at each variant site for the founder
 strains and experimental populations across each sequenced timepoint.
 Columns include: * Column 1: Chromosome (CHROM) * Column 2: Position (POS)
 * Column 3: Reference allele (ref) * Column 4: Alternate allele (alt) *
 Columns 5-28: Alternating allele frequency (alt_ETH_hap_X_Y_00) and
 coverage (N_ETH_X_Y_00) for founder haplotypes and X and Y are the
 haplotype identifiers. * Columns 29-30: Alternating allele frequency
 (alt_ETH_anc_12SH_12) and coverage (N_ETH_anc_12SH_12) for the ancestral
 population. * Columns 31-390: Alternating allele frequency (alt_ETH_X_Y)
 and coverage (N_ETH_X_Y) for experimental populations where and X is the
 replicate number and Y is the timepoint/cycle. ###
 Selection_Coefficient_Analysis This folder contains Bait-ER output files
 with estimated selection coefficients for SNPs in each treatment group.
 Inputs for Bait-ER were generated by extracting relevant portions of the
 filtered SNP table available in the SNP_Tables folder and converting them
 to sync format. Output files include: * `control_BaitER_results.txt` *
 `moderate_BaitER_results.txt` * `high_BaitER_results.txt` Columns in the
 output files include: * Column 1: Chromosome identifier (chromosome) *
 Column 2: SNP position on the chromosome (position) * Column 3: Reference
 allele (reference) * Column 4: Standard error of the selection estimate
 (sigma) * Column 5: Log Bayes Factor for selection (logBF) * Column 6:
 Alpha parameter from Bait-ER model (alpha) * Column 7: Beta parameter from
 Bait-ER model (beta) ### Candidate_SNP_Identification This folder contains
 output files from an adapted **CMH (Cochran-Mantel-Haenszel)** test to
 identify candidate SNPs under selection across timepoints for each
 treatment. Output files include: * `CMH_Results_Controls_1v15.txt` - CMH
 results comparing control populations between cycles 1 and 15. *
 `CMH_Results_High_1v15.txt` - CMH results comparing high ethanol
 populations between cycles 1 and 15. * `CMH_Results_Moderate_1v15.txt` -
 CMH results comparing moderate ethanol populations between cycles 1 and
 15. Columns in the output files include: * Column 1: Chromosome identifier
 (chr) * Column 2: SNP position on the chromosome (pos) * Column 3: P-value
 indicating significance of allele frequency change (pval) ### SNP_Tables
 This folder contains tables of SNPs identified across the ancestral and
 experimental populations at each sequenced timepoint. Output files
 include: * `SNPtable_raw.txt` - Raw SNP frequency table. This table was
 generated by converting the merged VCF file and is provided here so that
 all filtering steps and SNP-level analyses can be fully reproduced. *
 `SNPtable_50X_scaled.txt` - Filtered and scaled SNP table adjusted for
 coverage, retaining only high-confidence sites. This SNP table serves as
 the primary input for most downstream genomic analyses. Columns include: *
 Column 1: Chromosome (chr) * Column 2: Position (pos) * Column 3:
 Reference allele (ref) * Column 4: Alternate allele (alt) * Columns 5-12:
 Alternating allele frequency (alt_ETH_anc_X_Y) and coverage
 (N_ETH_anc_X_Y) for the ancestral population where X is the ancestral
 population identifier and Y is cycle number. * Columns 13-372: Alternating
 allele frequency (alt_ETH_X_Y) and coverage (N_ETH_X_Y) for experimental
 populations where and X is the replicate number and Y is the
 timepoint/cycle. ## Data File Formats * File format(s): TXT * Missing
 values are indicated as: NA ## Relationship to Analysis Code The data in
 this Dryad repository are intended to be used with analysis scripts
 available on GitHub: **GitHub repository:**
 \[[https://github.com/mphillips67/Genomics-Ethanol-Stress-Outcrossing-Yeast](https://github.com/mphillips67/Genomics-Ethanol-Stress-Outcrossing-Yeast)] ## Software Requirements Reproducing the analyses requires: * R version 4.0.4 A complete list of required packages is provided in the GitHub repository