Data and coding files for: Experimental evolution under combined thermal-nutritional stress in Drosophila melanogaster results in evolved shifts in larval thermotolerance and thermal plasticity

README

We investigated how long-term adaptation to combined thermal-nutritional stress affects larval thermotoelrance and thermal plasticity. We assessed basal and induced cold and heat tolerance of larvae from nine *D. melanogaster *experimental evolution lines that were forced adapted to combinations of three temperatures (18°C, 25°C and 28°C) and three diets (standard, diluted and low protein:high carbohydrate (low P:C) diets) using laboratory natural selection.

Description of the data and file structure

This repository contains the following data and scripts:

• Viability data (".csv")
• R markdown scripts (".Rmd") containing code for data analyses and visualizations
• Data generated from analyses (".Rdata") for further analyses and visualizations

Data Files

• “EEL thermoplasticity.csv”: Contains all viability data from all thermal shock treatments in all nine selection lines.
• • vial_number: the number of vial
  • selection_line: selection line, a combination of selection treatment and replicate line
  • selection_treatment: selection treatment, a combination of selection temperature and selection diet
  • selection_temperature: selection temperatures (18= 18, 25 = 25°C, 28 = 28°C)
  • selection_diet: selection diets (A = standard diet, B = diluted diet, C = low P:C diet)
  • replicate_line: replicate line number
  • treatment: treatment, a combination of the type of thermal shocks (cold or heat) and hardening treatment (Yes or no)
  • treatment_type: type of thermal shocks (c = cold shock, h = heat shock, control = control)
  • hardening: presence of a hardening treatment (Y = Yes, N = No)
  • acute_shock: presence of an acute thermal shock (Y = Yes, N = No)
  • hardening_temperature: temperature of the hardening treatment (NA = not applicable, 0 = 0°C, 35 = 35°C)
  • hardening_hours: duration of the hardening treatment (NA = not applicatble, 2 = 2 hours, 1 = 1 hour)
  • treatment_temperature: temperature of the acute shock treatment (NA = not applicable, 0 = 0°C, 39 = 39°C)
  • treatment_hours: duration of the acute shock treatment (4 = 4 hours, 0.5 = 0.5 hour)
  • replicate vial: replicate vial number
  • block: block number
  • adult_eclosed: number of eclosed adults in the vial
  • female: number of eclosed female in the vial
  • male: number of eclosed male in the vial
  • unknown: number of gender-unidentified individual in the vial (empty cells means not applicable)
  • viability: number of eclosed adults / number of eggs deposited in the vial (20)
  • egg_deposited: number of eggs deposited in the vial
  • comment: comments
• “Pilot - EEL thermoplasticity_new.csv”: Contains all viability data from pilot thermal shock treatments in lines selected on standard diets at different temperatures.
• • vial_number: the number of vial
  • selection_treatment: selection treatment, a combination of selection temperature and selection diet
  • selection_temperature: selection temperatures (18= 18, 25 = 25°C, 28 = 28°C)
  • selection_diet: selection diets (A = standard diet, B = diluted diet, C = low P:C diet)
  • replicate_line: replicate line number
  • treatment: treatment, a combination of the type of thermal shock (cold or heat), hardening hours (duration of the hardening treatment) and treatment hours (duration of the acute shock)
  • treatment_type: type of thermal shock (c = cold shock, h = heat shock)
  • hardening: presence of hardening treatment (Y = Yes, N = No)
  • hardening_temperature: temperature of the hardening treatment (NA = not applicable, 0 = 0°C, 35 = 35°C)
  • hardening_hours: duration of the hardening treatment (NA = not applicatble, 2 = 2 hours, 1 = 1 hour)
  • treatment_temperature: temperature of the acute shock treatment (0 = 0°C, 39 = 39°C)
  • treatment_hours: duration of the acute shock treatment (0.25 = 0.25 hour, 0.5 = 0.5 hour, 1 = 1 hour, 2 = 2 hours, 4 = 4 hours, 5 = 5 hours, 6 = 6 hours)
  • replicate vial: replicate vial number
  • block: block number
  • adult_eclosed: number of eclosed adults in the vial
  • viability: number of eclosed adults / number of eggs deposited in the vial (20)
  • egg_deposited: number of eggs deposited in the vial

Code Scripts (.Rmd)

All code files are commented and annotated.

• ANOVA:
• • "EEL thermoplasticity analysis (control) sum to zero contrast.Rmd" for assessing the effect of selection temperature and selection diets on basal larval-adult viability
  • "EEL thermoplasticity analysis (heat) sum to zero contrast.Rmd" for assessing the effect of selection temperature and selection diets on basal and induced heat tolerance
  • "EEL thermoplasticity analysis (cold) sum to zero contrast.Rmd" for assessing the effect of selection temperature and selection diets on basal and induced cold tolerance
  • "Pilot - EEL thermoplasticity analysis heat (sum to zero contrast).Rmd" for determining suitable durations for heat hardening and heat shock treatments
  • "Pilot - EEL thermoplasticity analysis cold (sum to zero contrast).Rmd" for determining suitable durations for cold hardening and cold shock treatments
• Data visualization:
• • "ggplot (cold).Rmd" for figure 1 and 2
  • "ggplot (heat).Rmd" for figure 3
  • "Pilot ggplot - EEL thermoplasticity analysis cold.Rmd" for figure S1
  • "Pilot ggplot - EEL thermoplasticity analysis heat.Rmd" for figure S2

Data Files Generated from Analyses (.Rdata)

• Includes: "EEL_ctrlm.Rdata", "EEL_clm2.1.Rdata", and "EEL_hlm1.3.Rdata"
• Use of these data is included and annotated in the .Rmd files.

Code/Software

• R is required to run the coding scripts (".Rmd" files). The scripts were created using R version 2023.09.0.+463 (RStudio 2023.09.0+463 "Desert Sunflower" Release).
• Microsoft Excel can be used to view ".csv" files.