Data and coding files for: Assessing the effect of experimental evolution under combined thermal-nutritional stress on larval thermotolerance and thermal plasticity in Drosophila melanogaster

Full description

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
• R markdown in the HTML notebook format (.nb.html) containing code for data analyses and visualizations, and coding outputs
• 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" and "EEL thermoplasticity analysis (control) sum to zero contrast.nb.html" for assessing the effect of selection temperature and selection diets on basal larval-adult viability
  • "EEL thermoplasticity analysis (heat) sum to zero contrast.Rmd" and "EEL thermoplasticity analysis (heat) sum to zero contrast.nb.html" 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" and "EEL thermoplasticity analysis (cold) sum to zero contrast.nb.html" 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" and "Pilot - EEL thermoplasticity analysis heat (sum to zero contrast).nb.html" for determining suitable durations for heat hardening and heat shock treatments
  • "Pilot - EEL thermoplasticity analysis cold (sum to zero contrast).Rmd" and "Pilot - EEL thermoplasticity analysis cold (sum to zero contrast).nb.html" for determining suitable durations for cold hardening and cold shock treatments
• Data visualization:
• • "ggplot - cold and control.RMD" and "ggplot - cold and control.nb.html" for figure 1 and 2
  • "ggplot - heat.Rmd" and "ggplot - heat.nb.html" for figure 3 and figure S1
  • "Pilot ggplot - EEL thermoplasticity analysis cold.Rmd" and "Pilot ggplot - EEL thermoplasticity analysis cold.nb.html" for figure S2
  • "Pilot ggplot - EEL thermoplasticity analysis heat.Rmd" and "Pilot ggplot - EEL thermoplasticity analysis heat.nb.html" for figure S3

Data Files Generated from Analyses (.Rdata)

• Includes: "EEL_ctrlm.Rdata", "EEL_ctrlm_t.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 2024.12.1+563 (RStudio 2024.12.1+563 "Kousa Dogwood" Release).
• Microsoft Excel can be used to view ".csv" files.