DOI: 10.5281/zenodo.16400562
title: Supporting data for "Socially regulated developmental plasticity in the color pattern of an anemonefish"

description: 'field survey data.csv' - observed counts of juveniles on coral reefs which exhibited full or reduced white barring used in constructing Figure 1A.

'raw field observations and notes.xls' - Recorded notes from field surveys separated by year (tabs). Information includes site/location, depth, individual fish ID, species, bar number, cohabitation status, interactions, distance from nearest anemone, and additional comments.

'dev exp images.7z' - Compressed folder containing images of pre-treatment juveniles and those used in each environmental treatment and used for colour pattern area analysis in Figures 1B-E, and Figure 2B.

'dev exp dataset.csv' - data used for plotting (Figures 1D, 1E, Supplementary Figure 1) and statistical analyses of white bar area and standard length (SL_mm) in the environmental treatment experiment. Columns include information on photoID (fish image ID), round/replicate, treatment ('A' = Occupied Anemone, 'B' = Anemone, 'C' = Fake anemone, 'D' = Empty), sampled_age (38 or 62 days-post-hatch), number of pixels clustered as white (white_pix), black (black_pix), and orange (orange_pix).

'dev exp analyses.R' - R script for statistical analyses and plotting of developmental bar loss experiment data (Figures 1D, E, Supplementary Figure 1) comparing bar loss among environmental treatments and fish body size.

'sl ratio data.csv' - standard length ratios calculated per individual fish and the next largest fish in the group. Data used for calculating mean SL ratios in each treatment.

'skin DGE analysis.7z' - Compressed folder containing analysis result outputs, R-script, metadata, mapped read files and other required data files for performing the skin-level transcriptomic and DGE analyses (depicted in Figures 2A-F, 3A, 4A, 5A, 7C, 7D, Supplementary Figure 2):



R scripts for running both DGE analyses on 38dph and 62dph skin samples, and the plotting of normalized gene expression (heatmaps, boxplots).

gene_symbols.txt - for attributing gene IDs matching corresponding arbitrary target IDs from the A. clarkii reference transcriptome.

metadata_1.txt - Metadata for 38dph samples (excluding pre-treatment samples).

metadata_2.txt - Metadata for 38dph samples (including pre-treatment, 'PT' samples).

metadata_3.txt - Metadata for 38dph samples (grouped by PC1 similarity and body length, with larger 'A' and  smaller 'B').

metadata_4.txt - Metadata for 38dph samples (grouped by PC2 similarity and live host anemone status).

metadata_5.txt - Metadata for 62dph samples.

pairwisecorrelationvalues_38dph.csv - Spearman rank correlation values calculated between all paired comparisons of 38dph samples.

pairwisecorrelationvalues_62dph.csv - Spearman rank correlation values calculated between all paired comparisons of 62dph samples.

PCA_results_38dph.csv - PCA results for 38dph samples.

PCA_results_62dph.csv - PCA results for 62dph samples.

1.5lfc_DGE_compilation_38dph.xls - Differentially expressed genes sorted into separate tabs by each treatment comparison for 38dph samples.

1.5lfc_DGE_compilation_62dph.xls - Differentially expressed genes sorted into separate tabs by each treatment comparison for 62dph samples. 

Aclarkii_GO_annotation.txt - Gene ontology annotation file with gene target IDs matching that of the A. clarkii reference transcriptome.

GO_enrichment_compilation_38dph.xls - Top 1000 gene ontology terms returned from GO enrichment analyses with separate tabs per treatment comparison for 38dph samples.

GO_enrichment_compilation_62dph.xls - Top 1000 gene ontology terms returned from GO enrichment analyses with separate tabs per treatment comparison for 62dph samples.

 skin mapped reads - folder containing individual mapped read (.H5 and .TSV) files per sample.

gene lists - subfolder containing (.txt) files for specific gene sets. Each file contains two columns with 'gene_id' and corresponding reference tome 'target_id'.


'whole body DGE analysis.7z' -  Compressed folder containing R-script, metadata, and mapped read files for performing the whole fish transcriptomic and DGE analysis used in making Figure 5B and Supplementary Figure 6:



R script for running the DGE analyses for whole body fish samples, and the plotting of normalized gene expression (heatmaps, boxplots).

metadata_6.txt - Sample information for whole body samples.

whole body mapped reads - folder containing individual mapped read files per sample.


'TEM images.7z' - Compressed folder containing both multipanel (stitched) transmission electron microscopy images in fish skin and higher magnification images used in figures of iridophores and their nuclei (Figure 3B). Left (L) and right (R) side images of sectioned fish are also included.

'TEM cell size data.csv' - Chromatophore cell area (in square microns) measured in TEM micrographs of A. frenatus skin in different stages of bar loss used in statistical comparisons of cell size (depicted in Figure 3D).

 'TEM total cover data.csv' - Data collected from TEM micrographs on the relative surface area coverage per chromatophore type normalised by total sectioned skin area in the body bar skin of A. frenatus (depicted in Figure 3C, Supplementary Figure 3).

'TEM platelet size data.csv' - Iridophore guanine crystal platelet dimensions (longest dimension = length, shortest dimension = width) measured in the body bar region skin of A. frenatus during different stages of bar loss. Units in microns (depicted in Figure 3E).

'TEM cell analyses.R' - R script for the plotting (Figures 3C-E) and statistical analyses of chromatophore abundance and size in A. frenatus skin.

'TUNEL data.csv' - Measured fluorescence signals from micrographs of TUNEL treated skin sections. Data includes the area per individual measured (cell) area, mean intensity, integrated density (IntDen), background intensity (bg_mean), and corrected total cellular fluorescence (CTCF) plotted in Figure 4B and Supplementary Figure 4.

'TUNEL analyses.R' - R script for plotting and summary statistics of cell fluorescence data used in making bar plot in Figure 4B and Supplementary Figure 4.

'TA1 TUNEL images.7z' - Fluorescence microscope images taken of sectioned A. frenatus skin (for fish TA1) treated with or without TUNEL reaction mix depicted in Figure 4B.

'TA2 TUNEL images.7z' - Fluorescence microscope images taken of sectioned A. frenatus skin (for fish TA2) treated with or without TUNEL reaction mix depicted in Supplementary Figure 4.

'IHC images.7z' - Compressed file containing brightfield micrographs of immunostained skin sections treated with or without (control) cleaved-caspase 3 antibody depicted in Figure 4C and Supplementary Figure 5.

'zvad exp data.csv' - Raw dataset for the Z-VAD-FMK treatment experiment depicted in Figures 4D, 4E, and Supplementary Figure 5.

'zvad exp data formatted.csv' - Dataset for the Z-VAD-FMK treatment experiment re-formatted for statistical analyses and individual-based (paired) comparisons.

'zvad exp analysis.R' - R script for conducting statistical analyses and plotting of Z-VAD-FMK experiment (Figures 4D, 4E, and Supplementary Figure 5).

'behav exp 1 formatted data.csv' - Dataset for behaviour experiment 1 (intraspecific trials) re-formatted for statistical analyses.

'behav exp 1 plot data.csv' - Unformatted data for behaviour experiment 1 plotting of Figure 6B.

'behav exp 2 formatted data.csv' - Dataset for behaviour experiment 2 (interspecific trials) re-formatted for statistical analyses.

'behav exp 2 plot data.csv' - Unformatted data for behaviour experiment 2 plotting of Figure 6C.

'behav exp overall aggression by sex.csv' - Combined dataset for behaviour experiments 1 & 2 with agonistic behaviour counts separated by individual adult territory holders (depicted in Supplementary Figure 7).

'behav exp analyses.R' - R script for running all statistical analyses and plotting of behaviour experiments 1 & 2 (Figures 6B, C, and Supplementary Figure 7).

'ecological data.xls' - Raw compiled ecological variables dataset with additional notes and separate tabs for iNaturalist observations (links and number of fish per curated observation), and primary literature references (data used in making Figures 6 D-F). 

'phylodata1.txt' - Data for phylogenetic trait mapping of bar loss during ontogeny ('1' = Yes, '2' = No).

'phylodata2.txt' - Data for GLS/PGLS analyses on bar loss during ontogeny, and mean group size, and max group size.

'phylodata3.txt' - Data for GLS/PGLs analyses on bar loss during ontogeny and number of reproductive anemone host species, and total host anemone species.

'phylogenetic analyses.R' - R script for performing the phylogenetic mapping of bar loss during ontogeny, ancestral state reconstruction, GLS/PGLS analyses, and generating plots/Figures 6D-F.

Note that the anemonefish species tree used in the phylogenetic analyses was from Gaboriau et al. (2025) and can be downloaded from: https://zenodo.org/records/14262748

'dev exp initial fish sizes.xls' - Fish size data in standard length (mm) measured per treatment at 18dph immediately prior to commencing the experiment (in 'treatment' tab) and for the four randomly sampled baseline juveniles ('baseline' tab).

'behavexp_container_spectransm_01.txt' - Raw spectral transmission measurement #1 through the plastic containers in the behaviour experiment and used for calculating average values (depicted in Supplementary Figure 8).

'behavexp_container_spectransm_02.txt' - Raw spectral transmission measurement #2 through the plastic containers in the behaviour experiment and used for calculating average values (depicted in Supplementary Figure 8).

'behavexp_container_spectransm_03.txt' - Raw spectral transmission measurement #3 through the plastic containers in the behaviour experiment and used for calculating average values (depicted in Supplementary Figure 8).