Data for: Behavior evolves as a correlated response to selection on cuticle color in Drosophila melanogaster and D. simulans

Ruckman, Sarah 1 ; Duffy, Alexandra2; Montes Mendez, Paulina1; McCaffery, Katelyn1; Miller, Samuel1; Crews, Addison1; Tan, Nicholas1; Campbell, Lauren1; March, Ashley1; Brown, Elizabeth1; Houle, David1

Published Jun 15, 2026 on Dryad. https://doi.org/10.5061/dryad.f4qrfj79z

Data files

Jun 15, 2026 version files 735.39 KB

activity_ALL.csv

62.21 KB
Binning.csv

1.23 KB
DAM_all.csv

179.39 KB
DL_Contrasts.csv

1.81 KB
Exp_Evo_All.csv

397.30 KB
geotaxis_ALL.csv

77.06 KB
README.md

10.71 KB
tri_means.csv

5.70 KB

Abstract

Data from an experimental evolution study examining correlated responses to artificial selection on cuticle color in Drosophila melanogaster and D. simulans. Replicate populations of each species were selected for light or dark thoracic coloration over 16 generations, with unselected control lines maintained in parallel. Correlated responses were measured in aggression (generations 0, 5, 10, 15), basal activity (generation 12), geotaxis (generation 13), and total activity and sleep (generation 16). Thorax color was quantified as the mean grayscale value of the dorsal thorax using ImageJ. Files include individual-level data for each behavioral trait along with population-level color summaries and binning validation data. All analyses were conducted in R; code is available in the GitHub repository linked in our Related Works.

Data Description

This dataset accompanies an experimental evolution study in which replicate populations of Drosophila melanogaster and D. simulans were artificially selected for light or dark thoracic cuticle color over 16 generations, with unselected control lines maintained in parallel. Correlated responses to color selection were measured in aggression (generations 0, 5, 10, 15), basal activity (generation 12), geotaxis (generation 13), and total activity and sleep (generation 16). Thorax color was quantified as the mean grayscale value of the dorsal thorax from photographs analyzed in ImageJ (lower values = darker). The dataset includes individual-level behavioral and color measurements, population-level color summaries, divergence contrasts between selection lines, and binning validation data.

Files and Variables

Exp_Evo_All.csv

Individual-level data for thorax color and aggression across all generations, species, populations, selection lines, and sexes.

Variable	Description
`Species`	Species: `mel` = D. melanogaster, `sim` = D. simulans
`Rep`	Laboratory population replicate (`Houle`, `Houston`, `sim1`, `sim2`)
`Line`	Selection treatment: `Dark`, `Control`, `Light` (or `population` for generation 0)
`Sex`	`Male` or `Female`
`Gen`	Generation of selection: 0, 5, 10, or 15
`Number`	Individual ID within assay
`Trident`	Mean grayscale value of dorsal thorax (lower = darker)
`Agg`	Count of aggressive behaviors observed per trial
`RepN`	Population replicate number (1 or 2 per species)
`Treat`	Continuous treatment code: -1 (Light), 0 (Control), 1 (Dark)
`SpRep`	Population ID: `mel1`, `mel2`, `sim1`, `sim2`

tri_means.csv

Population-level means for thorax grayscale color by generation, species, population, selection line, and sex.

Variable	Description
`Species`	Species: `mel` or `sim`
`Rep`	Laboratory population replicate
`Gen`	Generation of selection
`Line`	Selection treatment: `Dark`, `Control`, `Light`
`Sex`	`Male` or `Female`
`mean`	Mean grayscale color value
`sd_value`	Standard deviation
`N`	Sample size
`se_value`	Standard error

DL_Contrasts.csv

Dark vs. Light contrasts in color and aggression by generation, population, and sex. Used for visualization of divergence trajectories over time.

Variable	Description
`ColorC`	Mean color contrast (Dark minus Light)
`ColorSE`	Standard error of color contrast
`AggC`	Mean aggression contrast (Dark minus Light)
`AggSE`	Standard error of aggression contrast
`Contrast`	Contrast type (D-L)
`Population`	Laboratory population replicate
`Species`	Species: `mel` or `sim`
`Gen`	Generation of selection
`Sex`	`Male` or `Female`

activity_ALL.csv

Individual-level basal activity data from open field arena assays at generation 12, including individual thorax color measurements.

Variable	Description
`Species`	Species: `mel` or `sim`
`Rep`	Laboratory population replicate
`Line`	Selection treatment: `Dark`, `Control`, `Light`
`Sex`	`Male` or `Female`
`Number`	Individual ID within assay
`Activity`	Number of grid lines crossed in open field arena (1 min)
`RepN`	Population replicate number
`Observer`	Observer who conducted the assay
`Treat`	Continuous treatment code: -1 (Light), 0 (Control), 1 (Dark)
`SpRep`	Population ID: `mel1`, `mel2`, `sim1`, `sim2`
`Color`	Mean grayscale value of dorsal thorax (lower = darker)

DAM_all.csv

Individual-level total activity and sleep data collected over 72 hours using the Drosophila Activity Monitor (DAM) system at generation 16. Note: individual color measurements were not taken for DAM individuals.

Variable	Description
`Species`	Species: `mel` or `sim`
`Rep`	Laboratory population replicate
`Line`	Selection treatment: `Dark`, `Control`, `Light`
`Treat`	Continuous treatment code: -1 (Light), 0 (Control), 1 (Dark)
`Sex`	`Male` or `Female`
`Number`	Individual ID
`RepN`	Population replicate number
`Total_Sleep`	Total sleep in minutes per day (5-min bouts of inactivity)
`Day_Sleep`	Daytime sleep in minutes per day
`Night_Sleep`	Nighttime sleep in minutes per day
`Total_Activity`	Total beam crossings per day
`Total_P_wake`	Proportion of time awake
`Total_Waking`	Waking activity rate
`Average_Bout_length`	Mean sleep bout length (min)
`Average_Bout_Number`	Mean number of sleep bouts per day
`Total_P_doze`	Proportion of time dozing

geotaxis_ALL.csv

Individual-level geotaxis data at generation 13, including individual thorax color measurements.

Variable	Description
`Species`	Species: `mel` or `sim`
`Rep`	Laboratory population replicate
`Line`	Selection treatment: `Dark`, `Control`, `Light`
`Sex`	`Male` or `Female`
`Number`	Individual ID within assay
`Geotaxis`	Raw time to climb 2 cm (s)
`RepN`	Population replicate number
`Gcutoff`	Time to climb 2 cm, censored at 60 s
`Yes/No`	Event indicator: 1 = climbed within 60 s, 0 = censored
`Observer`	Observer who conducted the assay
`Treat`	Continuous treatment code: -1 (Light), 0 (Control), 1 (Dark)
`SpRep`	Population ID: `mel1`, `mel2`, `sim1`, `sim2`
`Color`	Mean grayscale value of dorsal thorax (lower = darker)

Binning.csv

Validation data for the visual color binning method. A subset of 100 individuals were scored twice to assess repeatability of color assignments.

Variable	Description
`Photos`	Grayscale value from photograph
`Bin1`	Color bin assigned at time point 1 (0 = light, 1 = dark)
`Bin2`	Color bin assigned at time point 2 (0 = light, 1 = dark)

Missing Data

Missing data are represented as blank cells in Exp_Evo_All.csv, activity_ALL.csv, and geotaxis_ALL.csv. Empty cells represent data that were not collected and do not indicate a value of zero. Missing values will not interfere with the R scripts provided, as R handles both blank cells and NA natively.

Exp_Evo_All.csv — Trident (thorax color): A small number of individuals escaped, died, or had unusable photographs before color measurements could be taken.

Exp_Evo_All.csv — Agg (aggression): A small number of individuals escaped or died before aggression could be recorded.

activity_ALL.csv — Color: A small number of individuals died or escaped before photographs could be taken.

geotaxis_ALL.csv — Color: A small number of individuals died or escaped before photographs could be taken.

Code and Software

All analyses were conducted in R version 4.5.0. R scripts for all analyses are available at: https://github.com/sruckman/Exp_Evo_2024

Key packages: ggplot2, emmeans, car, MASS, glmmTMB, coxme, survival

Thorax color was quantified from photographs using ImageJ. Analysis protocols are described in the Supplemental Material of the associated publication.

Access Information

This dataset is made available under the Creative Commons Zero (CC0) license.

The associated publication is: Ruckman SN et al. (2026). Behavior evolves as a correlated response to selection on cuticle color in Drosophila melanogaster and D. simulans. Evolution.

R code for all analyses is available at: https://github.com/sruckman/Exp_Evo_2024