README: Evolutionary history and analysis of iridescent ultraviolet butterfly scales

Data for: Early phylogenetic origin and repeated ecological implementation of iridescent UV signaling in pierid butterflies

READ ME: directory structure and file descriptions

File Structure

vficarrotta_dryad_IUV_2022
|-Butterfly Photo Credits
| |-butterfly-photo-credits.ods
|-IUV Scoring QC
| |-data-tree_overlap_7-7-2022.csv
| |-genus_uv_7-7-2022.csv
| |-genus_uv_overlap_7-7-2022.csv
| |-uvg_7-7-2022.csv
| |-IUV_scoring_QC.r
|-Phylogeny and Ancestral State Reconstruction
| |-Phylogeny Build
| | |-bad_seqs.py
| | |-bad_taxa.py
| | |-Pieridae_7114.table
| | |-Pieridae_7114_final.outaln
| | |-Pieridae_7114_final_GB.csv
| | |-Pieridae_7114_SHL_names.tre
| |-ASR-IUV_analysis.r
| |-full-tree_species.csv
| |-Pieridae_7114_final_names_trim_dates_2-22-2022.tre
| |-plotting_ASR-IUV_output.r
| |-uv_mat_syn-edit-V2_2-22-22.csv
|-Ridge Density
| |-ridge_dens_master_v2.csv
| |-ridge_density_analysis.r
|-Species Lists
| |-gbif-species-list_synedit.csv
| |-master-sp-list_extant-only_7-7-2022.csv
|-Spectral Analysis
| |-IUV raw text files.gzip
| |-IUV_spec-analysis_5-22-22.r
|-Tables
| |-tables_master_7-7-2022.xlsx

Description of file contents

Butterfly Photo Credits

Credits for butterfly images in Figure 1 ordered by their numbers. (List of species names, photographers)

IUV Scoring QC

These files produce supplemental figure 2 which demonstrates the reduced dataset does not lose analytical power.

• data-tree_overlap_7-7-2022: all species in both the scored dataset and the constructed tree. (List of species names, UV scores)
• genus_uv_7-7-2022: all genera/species with IUV in dataset. (List of species names, UV scores according to whether UV is present in males, females or both (mutual))
• genus_uv_overlap_7-7-2022: all genera/species with IUV overlapping within the uv_mat_syn-editV2_2-55-55.csv UV scoring dataset and the Pieridae_7114_final_names_trim_dates_2-22-2022.tre tree. (List of species names, UV scores according to whether UV is present in males, females or both (mutual))
• uvg_7-7-2022: CSV containing the final species list with UV scores for plotting the quality check. The species are further scored on whether they are included in the tree (Pieridae_7114_final_names_trim_dates_2-22-2022.tre), the uv score dataset (uv_mat_syn-edit-V2_2-22-22.csv) or both. (List of species names, UV scores according to whether UV is present in males, females or both (mutual))
• IUV_scoring_QC: r code used to generate the plot using the above .csv files.

Phylogeny and Ancestral State Reconstructions

• bad_seqs.py: sequences dropped from the phylogenetic analysis (list of species names)
• bad_taxa.py: taxa dropped from the phylogenetic analysis (list of species names)
• Pieridae_7114.table: Genbank sequence metadata from PyPHLAWD analysis
• Pieridae_7114_final.outaln: Sparse supermatrix from PyPHLAWD
• Pieridae_7114_final_GB.csv: Genbank accessions for sparse supermatrix from PyPHLAWD
• Pieridae_7114_SHL_names.tre: Dated, named tree from congruify analysis
• ASR-IUV_analysis.r: R code for generating all ancestral state reconstruction models and analyses
• full-tree_species.csv: CSV of all species in tree (list of species names)
• Pieridae_7114_final_names_trim_dates_2-22-2022.tre: copy and renamed final tree from congruify
• plotting_ASR-IUV_output.r.r: R code for plotting Figure 1 tree, Figure
• uv_mat_syn-edit-V2_2-22-22.csv: full dataset of screened museum specimens for IUV (list of species names, UV scores according to whether UV is present in males, females or both (mutual))

Ridge Density

• ridge_dens_master_v2.csv: dataset of measured ridge density for plotting Figure 2B (List species names, density of ridges continuous values (ridges per micrometer))
• ridge_density_analysis.r: R code to generate plot in figure 2B

Species Lists

• gbif-species-list_synedit.csv: accepted species list of all described Pieridae including fossils (list of species names)
• master-sp-list_extant-only_7-7-2022.csv: accepted species list of all described Pieridae without fossils (list of species names)

Spectral Analysis

IUV raw text files.gzip: raw spectral data in .txt format. must be unzipped (species names, trial number, continuous reflectance data) IUV_spec-analysis.r: R code for wrangling and plotting spectral data

Tables

tables_master_7-7-2022.xlsx: spreadsheet with two panes. The first pane shows model scores of strict presence/absence and the estimated transition rates of the highest scoring model. The second pane shows model scores including male and female scores and the estimated transition rates of the highest scoring model. Both panes are published as tables in the full manuscript.

Sharing and Access

Contents are accessible at the following GitHub URL: https://github.com/vficarrotta/Pierid_IUV_2023