DOI: 10.5061/dryad.x3ffbg7t3
title: Data and coding files for: Within population plastic responses to combined thermal-nutritional stress differ from those in response to single stressors, and are genetically independent across traits in both males and females

description: Phenotypic plasticity helps animals to buffer the effects of increasing
 thermal and nutritional stress created by climate change. Plastic
 responses to single and combined stressors can vary among genetically
 diverged populations. However, less is known about how plasticity in
 response to combined stress varies among individuals within a population
 or whether such variation changes across life-history traits. This is
 important because individual variation within populations shapes
 population-level responses to environmental change. Here, we used isogenic
 lines of Drosophila melanogaster to assess plasticity of egg-to-adult
 viability and sex-specific body size for combinations of two temperatures
 (25°C or 28°C) and three diets (standard diet, low caloric diet, or low
 protein:carbohydrate ratio diet). Our results reveal substantial
 within-population genetic variation in plasticity for egg-to-adult
 viability and wing size in response to combined thermal-nutritional
 stress. This genetic variation in plasticity was a result of
 cross-environment genetic correlations that were often &lt; 1 for both
 traits, as well as changes in the expression of genetic variation across
 environments for egg-to-adult viability. Cross-sex genetic correlations
 for body size were weaker when the sexes were reared in different
 conditions, suggesting that the genetic basis of traits may change with
 the environment. Further, our results suggest that plasticity in
 egg-to-adult viability is genetically independent from plasticity in body
 size. Importantly, plasticity in response to diet and temperature
 individually differed from plastic shifts in response to diet and
 temperature in combination. By quantifying plasticity and the expression
 of genetic variance in response to combined stress across traits, our
 study reveals the complexity of animal responses to environmental change,
 and the need for a more nuanced understanding of the potential for
 populations to adapt to ongoing climate change.
description: Details are in the main article.
description: # Data and coding files for Within population plastic responses to
 combined thermal-nutritional stress differ from those in response to
 single stressors, and are genetically independent across traits in both
 males and females.
 [https://doi.org/10.5061/dryad.x3ffbg7t3](https://doi.org/10.5061/dryad.x3ffbg7t3) ## Description of the data and file structure We investigated within-population variation in plastic responses of viability and wing size to combined thermal-nutritional stress. We also examined the genetic correlations between viability and wing size, as well as the cross-sex genetic correlation in wing size. This repository contains the following data and scripts: * **Raw data of wings** (".tif" files) * **Wing area data** (".csv", generated by CoordGen8) * **Viability data** (".csv") * **R markdown scripts** (".Rmd") containing code for data analyses and visualizations * **Data generated from analyses** (".Rdata") for further analyses and visualizations ## Raw Data * **“.zip” files**: Contain all wing photos in ".tif" format and a scale bar photo for calculating the number of pixels/mm, unique for each ".zip" file. * **".tif" files**: Named as "treatment&isogenic line number_vial number&sex_individual number.tif" (e.g., "25A1_1F_1.tif"). * **Treatment names**: Combinations of temperature (25°C, 28°C) and diets (A = standard diet, B = diluted diet, C = low P:C diet). ## Data Files * **“isogenic_viability.csv”**: Contains all viability data. * **ID**: Unique ID for each vial * **Line**: Isogenic line number * **Block**: Experimental block * **Temperature**: Treatment temperatures (25 = 25°C, 28 = 28°C) * **Diet**: Treatment diets (A = standard diet, B = diluted diet, C = low P:C diet) * **Rep**: Replicate vial number * **Adult_eclosed**: Total number of adults eclosed in the vial * **Male**: Number of males eclosed in the vial * **Female**: Number of females eclosed in the vial * **Unknown**: Number of gender-unidentified individuals eclosed in the vial (empty cells mean not applicable) * **Viability**: Number of eclosed adults / number of eggs deposited in the vial (20) * **Egg_total**: Number of eggs deposited in the vial * **“wingsize_for_r_copy.csv”**: Contains all wing size data. * **Specimen ID**: Unique ID for each individual * **Temperature**: Treatment temperatures (25 = 25°C, 28 = 28°C) * **Diet**: Treatment diets (A = standard diet, B = diluted diet, C = low P:C diet) * **Treatment**: Combinations of temperature and diet * **Block**: Experimental block * **Line**: Isogenic line number * **Rep**: Replicate vial number * **Sex**: Gender of the individual (F = female, M = male) * **Ind_no**: Number of individuals of either male or female from one vial * **LM1_X** to **LM8_Y**: x and y coordinates of landmarks 1 to 8 * **Centroid_Size**: Centroid size in pixels * **Centroid_Size_mm**: Centroid size in mm (Centroid size in pixels divided by pixels/mm, calculated using the calibration photo for each ".zip" file) #### Code Scripts (.Rmd) All code files are commented and annotated. * **Log-likelihood tests**: * "Review_LRT_Viability_2nd review.Rmd" for viability * "Review_LRT_Wingsize.Rmd" for wing size * **Bayesian statistics, MCMCglmm**: * "Review_MCMCglmm_viability_binomial_2nd review.Rmd" for viability * "Review_MCMCglmm_wingsize_sex.Rmd" for wing size * **Data visualization**: * "Review_ggplot_figure2_2nd review.Rmd" for figure 2 * "Review_ggplot_figure3_2nd review.Rmd" for figure 3 * "Review_ggplot_figure4.Rmd" for figure 4 * "Review_ggplot_figure5.Rmd" for figure 5 * "Review_ggplot_figureS1.Rmd" to "Review_ggplot_figureS7.Rmd" for supplementary figures S1 to S7 * "Supplementary_tables_G-matrices.Rmd" for making the supplementary tables S1 to S5 ## Data Files Generated from Analyses (.Rdata) * 103 items in total. * Use of these data is included and annotated in the .Rmd files. ### Code/Software * Any landmarking software can be used for calculating wing size, using the calibration slide (scale bar) to calculate pixels/mm. * Landmarks are indicated in Figure 1 of the main article. * 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.