Data from: Non-parallel impacts of predators on the evolution of colouration plasticity in Trinidadian killifish
Data files
Sep 30, 2025 version files 59.46 MB
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2025_08_29_Analysis_script.R
56.27 KB
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all_killifish_colormap_calib.csv
50.53 MB
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Ecological_variables.csv
1.84 KB
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Killifish_sex_length.csv
24.46 KB
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README.md
4.41 KB
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Shape_files.zip
8.84 MB
Abstract
Animal colouration is a key trait affecting survival and reproduction, yet the evolutionary drivers of colouration plasticity remain poorly understood. Here, we examine how predation shapes both baseline colouration and physiological colouration plasticity in the Trinidadian killifish (Anablepsoides hartii). This species inhabits streams that vary in fish predator presence, creating a replicated natural experiment across three rivers. We hypothesised that fish from high-predation sites would exhibit lighter baseline colouration due to associations with open canopy and increased light, and that predation would select for stronger plasticity in background-induced colour change. We assessed colouration before and after exposure to black or white backgrounds and analysed variation by predation regime, river, and sex. Our results show that baseline colouration differed significantly by predation regime, river identity, and sex, with high-predation fish generally lighter. A. hartii also displayed strong plasticity, darkening on black backgrounds and lightening on white. However, the effect of predation on plasticity was inconsistent across rivers, suggesting that local ecological factors mediate these responses. Our study provides rare empirical evidence for both baseline and plastic variation in colouration driven by ecological context, offering new insight into how phenotypic plasticity evolves in response to environmental pressures like predation.
Dataset DOI: 10.5061/dryad.2547d7x39
Description of the data and file structure
Data and code supporting the article 'Local adaptation in colouration plasticity of Trinidadian killifish'. This primarily consists of 3 .csv files containing collected data regarding the focal individuals and surrounding ecological measurements. More specifically, all_killifish_colourmap_calib.csv contains the calibrated colour values for each fish, Ecological_variables.csv contains ecological measurement data and Killifish_sex_length.csv contains both the sex and length data for each individual. This dataset also contains the Shape files of Trinidad used to create Figure 1, which was downloaded from https://hub.arcgis.com/datasets/uwi::coastline-trinidad-and-tobago/about.
Files and variables
File: Ecological_variables.csv
Description: Ecological measurements of the focal sites
Variables
- Date: date measurement was taken (day, month, year)
- River: Which river was measured (AM = Arima, AP = Aripo & EC = El Cedro)
- Predation: Which regime was measured (HP = High Predation, KO = Killifish-only)
- sample: The sample taken, to distinguish within site variation
- water_temp: Water temperature in °C
- conductivity: Conductivity in µS
- oxygen_saturation: Oxygen saturation in %
- lux: light measured in Lux
- width_m: widest point of stream in m at that section
- depth_m: deepest point of stream in m at that section
- canopy_cover: estimated canopy cover in %
- time: time of day observed
- weather: approximate weather conditions at time of sample
- pH: pH values as measured in the stream
File: Killifish_sex_length.csv
Description: Supplementary file to add the covariates of sex and length
Variables
- File: Name of photo file for an individual fish
- Sex: The sex of the fish contained within (F = Female, M = Male, J = juvenile and not possible to sex)
- Length: The length of the fish in mm
File: all_killifish_colormap_calib.csv
Description: Primary data file for analysis
Variables
- : Column with file path to the associated photo. This is a redundant column
- specimen.factors: detailed file name for each individual photo, which is used in the code to provide identity and independent variables.
- r_interior1: the extracted colour value for the red colour channel at position interior 1
- g_interior1: the extracted colour value for the green colour channel at position interior 1
- b_interior1: the extracted colour value for the blue colour channel at position interior 1
- r_interior2: the extracted colour value for the red colour channel at position interior 2
- ...
- these columns continue for every position and produce too many columns to describe each one, but they all follow the same basic structure.
File: Shape_files.zip
Description: Zip file containing the shapefiles necessary to recreate 'Figure 1' in the associated manuscript (Elevation map of Trinidad with sampling sites identified). Shapefiles are vector-based geographic information system (GIS) data. They can be opened and used in any GIS software and in R or Python. A shapefile consists of multiple file types beyond the .shp (specifically, .cpg, .dbf, .prj, and .shx). The user only interacts directly with the .shp file but the other files need to be in the same directory. Specifically in this case the shapefiles refer to the coastline of Trinidad and Tobago.
File: 2025_08_29_Analysis_script.R
Description: Code to reproduce the analyses and each figure
Code/software
The code was created using R (R Core Team (2024). _R: A Language and Environment for Statistical Computing. R Foundation for 'statistical Computing, Vienna, Austria. https://www.R-project.org/.
The packages used with are:
'Car'
'ggplot2'
'tidyr'
'dplyr'
'MANOVA.RM'
'adegenet'
'emmeans'
'patchwork'
'cowplot'
'sf'
'terra'
'elevatr'
'grid'
'viridis'
'ggrepel'
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- The shapefiles were derived from https://hub.arcgis.com/datasets/uwi::coastline-trinidad-and-tobago/about
