DOI: 10.5061/dryad.r8mb0
title: Data from: Parallel trait adaptation across opposing thermal environments in experimental Drosophila melanogaster populations

description: Thermal stress is a pervasive selective agent in natural populations that
 impacts organismal growth, survival, and reproduction. Drosophila
 melanogaster exhibits a variety of putatively adaptive phenotypic
 responses to thermal stress in natural and experimental settings; however,
 accompanying assessments of fitness are typically lacking. Here, we
 quantify changes in fitness and known thermal tolerance traits in
 replicated experimental D. melanogaster populations following more than 40
 generations of evolution to either cyclic cold or hot temperatures. By
 evaluating fitness for both evolved populations alongside a reconstituted
 starting population, we show that the evolved populations were the best
 adapted within their respective thermal environments. More strikingly, the
 evolved populations exhibited increased fitness in both environments and
 improved resistance to both acute heat and cold stress. This unexpected
 parallel response appeared to be an adaptation to the rapid temperature
 changes that drove the cycling thermal regimes, as parallel fitness
 changes were not observed when tested in a constant thermal environment.
 Our results add to a small but growing group of studies that demonstrate
 the importance of fluctuating temperature changes for thermal adaptation
 and highlight the need for additional work in this area.
description: # Parallel trait adaptation across opposing thermal environments in
 experimental Drosophila melanogaster populations Dataset DOI:
 [10.5061/dryad.rn8pk0pp5](10.5061/dryad.rn8pk0pp5) ## Description of the
 data and file structure This dataset contains data from phenotypic assays
 conducted in Drosophila melanogaster experimental evolution populations. A
 Drosophila melanogaster natural population had been exposed to two
 opposing thermal environments with daily cycling between either 28/18°C
 (hot) or 20/10°C (cold) and evolved in the laboratory for more than 40
 generations. Data for several traits (fitness, thermal stress resistance,
 body size, and developmental time) were collected from both evolved
 populations in parallel to a reconstituted starting population. The assays
 were conducted at two different evolutionary timepoints in shared common
 garden environments. ### Files and variables #### File:
 DRYAD\_Evolution\_ms\_data.zip **Description:** The compressed archive
 DRYAD_Evolution_ms_data.zip contains the following data files:
 **Dmel_PO_parallel_Hot75_Cold43_fitness.txt** Raw data for the fitness
 phenotype: Counts of wild type (hot F75, cold F43, and reconstituted base
 population) and white-eyed progeny from the fitness assay after two
 generations in the fluctuating 18–28°C and 10–20°C and the constant 23°C
 common garden environments. This dataset includes combined female and male
 counts from days 5, 10, and 15, for two sub replicates within each of five
 replicates. This dataset was used as input for the R script
 fitness_plots_Dmel_Hot74Cold43_NEW.r
 **Dmel_parallel_Hot59_Cold34_coldshock.txt** Raw data for the cold shock
 phenotype: Counts of individuals from the hot-evolved F59, cold-evolved
 F34, and reconstituted base population that recovered from cold shock
 within a 60-minute interval. This dataset includes separate female and
 male counts, recorded per minute for each of eight assayed vials/Petri
 dishes across five replicates in the constant 23°C and the constant 15°C
 common garden environments. It was used as input for the R script
 Thermalshocks_plots_stats_Dmel_parallel.r
 **Dmel_parallel_Hot59_Cold34_development.txt** Raw data for the
 developmental time phenotype: Counts of pupae in the hot-evolved F59,
 cold-evolved F34, and reconstituted base populations, assayed in the
 constant 23°C and the constant 15°C common garden environments. The number
 of newly emerged pupae was recorded daily across five replicates, with
 four bottles (sub replicates) per replicate. The dataset was used as input
 for the R script Development_time_Dmel_parallel.r
 **Dmel_parallel_Hot59_Cold34_heatshock.txt** Raw data for the heat shock
 phenotype: Counts of individuals from the hot-evolved F59, cold-evolved
 F34, and reconstituted base population knocked down from heat shock within
 a 60-minute interval. This dataset includes separate female and male
 counts across five replicates in the constant 23°C and the constant 15°C
 common garden environments, recorded per minute in each of eight assayed
 200 mL plastic tubes. It was used as input for the R script
 Thermalshocks_plots_stats_Dmel_parallel.r
 **Dmel_parallel_Hot59_Cold34_leglength.txt** Raw data for the body size
 phenotype (leg length): Tibia length (measured as distance between tarsus
 and femur, in mm) for five replicates of the hot-evolved F59, cold-evolved
 F34, and reconstituted base population in the constant 23°C and the
 constant 15°C common garden environments. Females and males were measured
 separately, with 30 individuals each per replicate. This dataset was used
 as input for the R script Morphology_plots_stats_Dmel_parallel.r
 **Dmel_parallel_Hot59_Cold34_wingarea.txt** Raw data for the body size
 phenotype (wing area): Wing area (in mm2) for five replicates of the
 hot-evolved F59, cold-evolved F34, and reconstituted base population in
 the constant 23°C and the constant 15°C common garden environments.
 Females and males were measured separately, with 30 individuals each per
 replicate. This dataset was used as input for the R script
 Morphology_plots_stats_Dmel_parallel.r
 **Dmel_parallel_Hot75_Cold43_coldshock.txt** Raw data for the cold shock
 phenotype: Counts of individuals from the hot-evolved F75, cold-evolved
 F43, and reconstituted base population that recovered from cold shock
 within a 60-minute interval. This dataset includes separate female and
 male counts, recorded per minute for each of eight assayed vials/Petri
 dishes across five replicates in the constant 23°C and the constant 15°C
 common garden environments. It was used as input for the R script
 Thermalshocks_plots_stats_Dmel_parallel.r
 **Dmel_parallel_Hot75_Cold43_development.txt** Raw data for the
 developmental time phenotype: Counts of pupae in the hot-evolved F75,
 cold-evolved F43, and reconstituted base populations, assayed in the
 constant 23°C and the constant 15°C common garden environments. The number
 of newly emerged pupae was recorded daily across five replicates, with
 four bottles (sub replicates) per replicate. The dataset was used as input
 for the R script Development_time_Dmel_parallel.r
 **Dmel_parallel_Hot75_Cold43_heatshock.txt** Raw data for the heat shock
 phenotype: Counts of individuals from the hot-evolved F75, cold-evolved
 F43, and reconstituted base population knocked down from heat shock within
 a 60-minute interval. This dataset includes separate female and male
 counts across five replicates in the constant 23°C and the constant 15°C
 common garden environments, recorded per minute in each of eight assayed
 200 mL plastic tubes. It was used as input for the R script
 Thermalshocks_plots_stats_Dmel_parallel.r
 **Dmel_parallel_Hot75_Cold43_leglength.txt** Raw data for the body size
 phenotype (leg length): Tibia length (measured as distance between tarsus
 and femur, in mm) for five replicates of the hot-evolved F75, cold-evolved
 F43, and reconstituted base population in the constant 23°C and the
 constant 15°C common garden environments. Females and males were measured
 separately, with 30 individuals each per replicate. This dataset was used
 as input for the R script Morphology_plots_stats_Dmel_parallel.r
 **Dmel_parallel_Hot75_Cold43_wingarea.txt** Raw data for the body size
 phenotype (wing area): Wing area (in mm2) for five replicates of the
 hot-evolved F75, cold-evolved F43, and reconstituted base population in
 the constant 23°C and the constant 15°C common garden environments.
 Females and males were measured separately, with 30 individuals each per
 replicate. This dataset was used as input for the R script
 Morphology_plots_stats_Dmel_parallel.r Missing values in all datasets are
 indicated by "NA." ## Code/software The compressed archive
 DRYAD_Evolution_ms_data.zip contains the following data files:
 **Development_time_Dmel_parallel.r** R script to analyze the developmental
 time data using a generalized mixed model as described in the Material and
 Methods. The output includes tables of statistical tests and plots.
 **Morphology_plots_stats_Dmel_parallel.r** R script to analyze the
 morphological data (tibia length and wing area) using a generalized mixed
 model as described in the Material and Methods. The output includes tables
 of statistical tests and plots.
 **Thermalshocks_plots_stats_Dmel_parallel.r** R script to analyze the
 thermal stress resistance data (heat and cold stress) using a generalized
 mixed model as described in the Material and Methods. The output includes
 tables of statistical tests and plots.
 **fitness_plots_Dmel_Hot74Cold43_NEW.r** R script to analyze the fitness
 data using a generalized mixed model as described in the Material and
 Methods. The output includes tables of statistical tests and plots. The
 software required to run the above R scripts is described in the
 associated manuscript: "All analyses were performed using R (version
 3.0.1; R Core Team 2013). The GLMMs used the lme4 package (version 1.0‐4;
 Bates et al. 2013) with subsequent significance testing performed via the
 ANOVA function from the car package (version 2.0‐19; Fox and Weisberg
 2011). Parameters were estimated using restricted maximum likelihood
 (i.e., the “REML” option). Contrasts used the phia package (version 0.1‐5;
 De Rosario‐Martinez 2013), with the “Holm” method (Holm 1979) being used
 to correct for multiple testing."