Data and Scripts to Support the Peer-Review Process

Repository Overview This repository accompanies the published study and contains all relevant scripts and datasets organized by analytical step. Each folder corresponds to a specific component of the analysis and is described below. 1. phylogeny/ — Lagomorpha Phylogeny Files: NodeDated_Allspp_1000.tre: A set of 1,000 dated phylogenetic trees. lagomorpha_mcc.tre: Maximum clade credibility (MCC) tree computed from the tree set. 2. final_dataset/ — Species-Level Dataset File: final_df.csv: Final dataset compiling species-level coloration and environmental variables. Key columns: Taxonomy & Metadata: species_name: Scientific name. family: Taxonomic family (e.g., Leporidae, Ochotonidae). pic_num: Number of photos used per species. pelage_change: Indicates if the species undergoes seasonal coat color change. color_inputation: Indicates whether coloration values were imputed. Coloration Metrics: Lightness: rgb_mean, rgb_median, rgb_sd cie_l_mean, cie_l_median, cie_l_sd hsv_v_mean, hsv_v_median, hsv_v_sd Redness: redness_mean, redness_median, redness_sd Environmental Variables: temp: Mean annual temperature (°C) precipitation: Mean annual precipitation (mm) forest_struct: Forest vertical structure index uv_b: UV-B radiation Geographic Data: latitude, longitude: Centroid coordinates of each species’ range 3. color_extraction/ — Specimen-Level Color Estimates Files: lightness_specimens.csv: Lightness values for individual photos. redness_specimens.csv: Redness values for individual photos. 4. ancestral_reconstruction/ — Ancestral Color Estimation File: ancestral_reconstruction.R: Script to estimate ancestral states for lightness and redness. Output: Reproduces Figure 1 of the main manuscript. 5. phylogenetic_regression/ — Bayesian Phylogenetic Regression Files: brms_darkness.R: Bayesian model for analyzing lightness. brms_redness.R: Bayesian model for analyzing redness. Output: Reproduces Figures 2 and 4 of the main manuscript. 6. spatial_coloration/ — Geographic Visualization of Coloration File: maps.R: Script for mapping species coloration based on geographic centroids, highlighting differences between Leporidae and Ochotonidae. Output: Reproduces Figures 3 and 5 of the main manuscript.