DOI: 10.5061/dryad.8931zcrx3
title: Evolutionary history and analysis of iridescent ultraviolet butterfly scales

description: Iridescent ultraviolet (IUV) patterns on pierid butterfly wings are
 phenotypic adaptations commonly used as sexual signals, generated by
 scales with ultrastructural modifications. Pierid IUV patterns are
 sexually dichromatic, with reduced size in females, where conspicuous
 sexual signaling balances courtship against ecological predation. There
 have been no phylogenetic reconstructions of IUV within Pieridae and
 little morphological characterization of phenotypic diversity. Our
 genus-wide characterization of IUV revealed the uniform similarity of
 stacked lamellar ridges on the dorsal surface of cover scales. We tested a
 hypothesis of single versus multiple origins by reconstructing a phylogeny
 of 534 species (~43.2% described species), with all genera represented,
 and a trait matrix of 734 species (~59.4%) screened for IUV. A single,
 early dimorphic origin of IUV followed by several losses and gains
 received strong support, concluding that IUV patterns and structural
 coloration are old traits. Collectively, these results support the
 homology of IUV scales and patterns that diversified within several
 lineages, suggesting an interplay between female-mediated sexual selection
 and ecological predatory selection.
description: Museum Scoring: Performed using a modified ultraviolet detecting
 camera and black light light source on museum specimens to score for
 presence/absence. SEM images: Wing samples were mounted
 to stubs using copper tape and imaged using an FEI Teneo LV SEM
 Ridge Density: SEM images of wing scales were measured in
 photoshop and analyzed in R. Phylogeny: Molecular
 sequences were scraped from Genbank. Processed using python and bash
 scripts. Analysis performed using RAxML. Spectral Data:
 collected using an Ocean Optics spectrophotometer. Analyses performed in
 R.
description: # 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