Data from: Avoiding dead ends: the experimental evolution of constraint as adaptation to environmental variation
Data files
Nov 10, 2025 version files 41.67 KB
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fitness_rawdata.xlsx
10.97 KB
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hst_rawdata.xlsx
11.20 KB
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masterdata_updated_v2.xlsx
12.32 KB
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README.md
7.17 KB
Abstract
A bet-hedging strategy is suboptimal over short timescales, but optimal over long time scales because it buffers temporal variance in fitness. However, it is unclear how such strategies can persist when selection is expected to purge suboptimal traits in the short term. It has been proposed that the persistence of bet hedging is possible only if adaptive evolution is constrained in the short-term (Simons, 2002). To test the constraint-as-adaptation hypothesis, we take an experimental evolution approach using Saccharomyces cerevisiae and predict that evolution under reduced-frequency detrimental events results in an increase in evolution-resistant bet-hedging. Specifically, we evolve bet-hedging by imposing fluctuating selection through repeated heat shocks separated by intervening benign environments in which the frequency of extreme environments is reduced across two sequential evolution regimes (Regimes A and B). Then, to measure evolved constraints lines from both regimes are further evolved under extended benign conditions for ~150 generations and tested for the loss of heat shock tolerance. This dataset provides heat shock tolerance and competitive fitness data for replicate lines evolved in both regimes, and for the T1 ancestor. This dataset also provides these trait measurements after the replicate lines from both regimes are further evolved under extended benign conditions.
https://doi.org/10.5061/dryad.zs7h44j9b
Heat shock tolerance & relative fitness data – EoR-A (Generation 0, 150), EoR-B (Generation 0, 150), T1 ancestor- Saccharomyces cerevisiae
Description of the data and file structure: masterdata_updated
Heat Shock Tolerance (hst):
This was measured as % Survival when exposed to a transient 54 °C heat shock for 75 minutes. Cell survival was measured by plating both heat-shocked and non-heat-shocked samples on YPD. Heat shock tolerance was measured for each replicate line, and at each time point. The T1 ancestor was measured 6 times. HST was measured as duplicate technical replicates (hst_techrep1, hst_techrep2)
Fitness under benign conditions (fitness):
Fitness under benign conditions was measured using a reference strain, YIR044CΔ with a BY4741 background (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0). Competition experiments were performed in Synthetic Defined Media + (His, Leu, Met, Ura) for 48 hours. The SDM was supplemented with amino acids to account for auxotrophies in the reference strain. Relative fitness was measured for each replicate line, and at each time point. The T1 ancestor was measured 8 times.
Files and variables
File: masterdata_updated_v2.xlsx
Description: Data file containing trait measurements
Variables
- Regime: Regime includes lines evolved in the two regimes (A and B) and the T1 ancestor. The T1 ancestor was used to compare trait measurements after evolution in Regimes A and B. The replicate lines had an evolutionary history of being evolved previously either in only Regime A for ~100 generations (A) or in both Regimes A & B for ~100 generations (B). Regime A consisted of high frequency of heat shocks applied once every ~8 generations. Regime B consisted of low frequency heat shocks applied once every ~50 generations. Experimental evolution was performed in Synthetic Defined Media.
- Replicate: 8 replicate lines from the two treatments (evolutionary histories).
- Time: This includes two time points -Generation 0 and Generation 150 of the trait persistence assay. An additional timepoint of Generation 100 is also included for the heat shock assays. After evolution in Regimes A and B, the 8 replicate lines from the end of both regimes were further evolved under constant benign conditions for 150 generations to assay for the loss of heat shock tolerance and concomitant gain in relative fitness.
- hst: Heat Shock Tolerance was measured as % Survival when exposed to a transient 54 °C heat shock for 75 minutes. Cell survival was measured by plating both heat shocked and non- heat shocked samples on YPD. Heat shock tolerance was measured for each replicate line, and at each time point. The T1 ancestor was measured 6 times. HST was measured as duplicate technical replicates (hst_techrep1, hst_techrep2)
- hst_techrep1, hst_techrep2: Two technical replicates for each measurement of heat shock tolerance.
- fitness: Fitness under benign conditions was measured using a reference strain, YIR044CΔ with a BY4741 background (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0). Competition experiments were performed in Synthetic Defined Media + (His, Leu, Met, Ura) for 48 hours. The SDM was supplemented with amino acids to account for auxotrophies in the reference strain. Relative fitness was measured for each replicate line, and at each time point. The T1 ancestor was measured 8 times.
File: hst_rawdata.xlsx
Description: Data file containing raw data for heat shock tolerance measurements
Variables
- Regime: Regime includes lines evolved in the two regimes (A and B) and the T1 ancestor. The T1 ancestor was used to compare trait measurements after evolution in Regimes A and B. The replicate lines had an evolutionary history of being evolved previously either in only Regime A for ~100 generations (A) or in both Regimes A & B for ~100 generations (B). Regime A consisted of high frequency of heat shocks applied once every ~8 generations. Regime B consisted of low frequency heat shocks applied once every ~50 generations. Experimental evolution was performed in Synthetic Defined Media.
- Replicate: 8 replicate lines from the two treatments (evolutionary histories).
- Time: This includes two time points -Generation 0 and Generation 150 of the trait persistence assay. An additional timepoint of Generation 100 is also included for the heat shock assays. After evolution in Regimes A and B, the 8 replicate lines from the end of both regimes were further evolved under constant benign conditions for 150 generations to assay for the loss of heat shock tolerance and concomitant gain in relative fitness.
- control_1, control_2: The non-heat shocked sample used to calculate % Survival
- hs_1a, hs_1b: First technical replicate of the heat shocked sample. This measurement was done in duplicate to count a sufficient number of cells.
- hs_1a, hs_1b: Second technical replicate of the heat shocked sample. This measurement was done in duplicate to count a sufficient number of cells.
File: fitness_rawdata.xlsx
Description: Data file containing raw data for competition assay measurements
Variables
- Regime: Regime includes lines evolved in the two regimes (A and B) and the T1 ancestor. The T1 ancestor was used to compare trait measurements after evolution in Regimes A and B. The replicate lines had an evolutionary history of being evolved previously either in only Regime A for ~100 generations (A) or in both Regimes A & B for ~100 generations (B). Regime A consisted of high frequency of heat shocks applied once every ~8 generations. Regime B consisted of low frequency heat shocks applied once every ~50 generations. Experimental evolution was performed in Synthetic Defined Media.
- Replicate: 8 replicate lines from the two treatments (evolutionary histories).
- Time: This includes two time points -Generation 0 and Generation 150 of the trait persistence assay. An additional timepoint of Generation 100 is also included for the heat shock assays. After evolution in Regimes A and B, the 8 replicate lines from the end of both regimes were further evolved under constant benign conditions for 150 generations to assay for the loss of heat shock tolerance and concomitant gain in relative fitness.
- initial_ypd_1, initial_ypd_2: The initial total number of cells (two technical replicates).
- initial_g418_1, initial_g418_2: The initial number of cells of the reference strain (two technical replicates).
- final_ypd_1, final_ypd_2: The final total number of cells (two technical replicates).
- final_g418_1, final_g418_2: The final number of cells of the reference strain (two technical replicates).
Code/software
Data is in .xlsx format.
Code used to analyse this data is found alongside this dataset. The code includes both parametric and non-parametric analyses for evolved constraint as well as for changes in trait values after evolution in either regime.
Data was collected from trait assays that were run simultaneously for all strains. Lines from the end of Regime A (EoR-A) and from the end of Regime B (EoR-B) were originally evolved from the T1 Ancestor which has an S288C background (MATα SUC2 gal2 mal2 mel flo1 flo8-1 hap1 ho bio1 bio6). The sequential experimental design implies that evolution proceeded along: T1 Ancestor --> Regime A (8 replicate lines) --> Regime B (8 replicate lines).
Heat Shock Tolerance was measured as % Survival on exposure to a transient 54°C heat shock for 75 mins.
Relative fitness was calculated using a competitive fitness assay with a reference strain, YIR044CΔ with a BY4741 background (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0). This strain has the pseudogene YIR044C deleted and replaced with a gene conferring G418 resistance—used as a selectable marker for this assay. Proportions of focal strain/test population relative to the reference strain both before and after the competition were determined by plating on YPD agar with and without G418. Relative fitness was calculated as described in Wong et al. (2012), where the selection coefficient was determined using the following equation. Fitness w was calculated as 1+ s.
Experimental evolution and heat shock tolerance assays were performed in Synthetic Defined Media (SDM) containing 6.7 g of Yeast Nitrogen Base (without amino acids with ammonium sulfate) and 2% dextrose per liter.
Competition experiments were performed in SDM+ Histidine (10 mg/L), Leucine (30 mg/L), Methionine (10 mg/L), Uracil (10 mg/L) to account for auxotrophies in the reference strain.
- Raghu, Shravan Ram; Smith, Myron; Simons, Andrew (2025). Data from: Avoiding dead ends: the experimental evolution of constraint as adaptation to environmental variation. Zenodo. https://doi.org/10.5281/zenodo.7060143
- Raghu, Shravan Ram; Smith, Myron; Simons, Andrew (2025). Data from: Avoiding dead ends: the experimental evolution of constraint as adaptation to environmental variation. Zenodo. https://doi.org/10.5281/zenodo.7060142
- Raghu, Shravan; Smith, Myron; Simons, Andrew (2022). Avoiding dead ends: the experimental evolution of constraint as adaptation to environmental variation in Saccharomyces cerevisiae [Preprint]. Springer Science and Business Media LLC. https://doi.org/10.21203/rs.3.rs-1200104/v1
- Raghu, Shravan R.; Smith, Myron L.; Simons, Andrew M. (2026). Avoiding dead ends: the experimental evolution of constraint as adaptation to environmental variation. Proceedings of the Royal Society B Biological Sciences. https://doi.org/10.1098/rspb.2025.1913