DOI: 10.5061/dryad.hdr7sqvwn
title: Data from: Camouflage, conspicuousness, and inducible color change in a polymorphic, sexually dichromatic frog

description: Sexual dichromatism is relatively rare in anuran amphibians (frogs and
 toads) but is striking and prevalent in the African reed frogs
 (Hyperoliidae). In sexually dichromatic hyperoliids, males and females
 exhibit shared coloration post-metamorphosis, but at the onset of
 maturity, females undergo a change in color and/or color pattern, whereas
 males typically retain the juvenile coloration. Hypothesized functions of
 dichromatism in reed frogs include sexual niche partitioning such that
 males and females use different habitats and their different colorations
 provide more effective camouflage in their respective habitats, or
 alternatively, that color patterns play a role in sex and/or mate
 recognition in dense breeding choruses. To test these hypotheses, we
 characterized several aspects of natural history, ecology, and physiology
 in a population of the sexually dichromatic forest reed frog (Hyperolius
 tuberculatus) on Bioko Island, Equatorial Guinea. This dataset includes 1)
 dorsal reflectance measurements for male and female H. tuberculatus and
 reflectance measurements of the substrates the frogs were found on, 2)
 microspectrophotometry measurements of H. tuberculatus photoreceptors, and
 3) code and custom visual models used to conduct visual modeling analyses
 using the R package pavo (Maia et al. 2019).
description: # Data from: Camouflage, conspicuousness, and inducible color change in a
 polymorphic, sexually dichromatic frog Dataset DOI:
 [10.5061/dryad.hdr7sqvwn](10.5061/dryad.hdr7sqvwn) ## Description of the
 data and file structure Microspectrophotometry of reed frog (*Hyperolius
 tuberculatus*) photoreceptors, reflectance measurements of reed frogs and
 the substrates they occur on, and code to conduct visual modeling analyses
 using the package *pavo* in R.  ### Files and variables #### File:
 ReedfrogMSP.zip **Description:** Microspectrophotometry measurements of
 rod and cone photoreceptors for one male and one female *Hyperolius
 tuberculatus*. For detailed methods refer to corresponding publication.
 Data presented here include 1) a summary of the characteristics of each
 cell scanned in each individual, and 2) raw and processed data from each
 scan. **1. Htuberculatus_msp.csv** This file contains summary data from
 each rod and cone scanned in each specimen of *H. tuberculatus* . Each row
 represents data from a single scan of a single rod or cone. Columns are as
 follows: * Specimen: Specimen number of archived specimen at the Cornell
 University Museum of Vertebrates * Stage (Sex): Life-history stage (here,
 all adult) and sex of the specimen for each scan. * Prep: Preparation of
 the retina used for MSP scans - here, all scans were taken from the first
 prep of each specimen’s eye and further preparations were not made. *
 Specimen: Tally of frog individual specimens examined for each species,
 stage, and sex. Here, only 1 individual male and 1 individual female were
 examined. * Class: Region of the visual spectrum where the scanned visual
 pigment peaks. G = green, Y = yellow, B = blue * Cell type: Type of
 photoreceptor cell scanned, identified under the microscope by morphology
 of the cell. C = cone, R = rod. * Data_file: File name of the raw data
 file associated with each scan. * Left: Weighting on left side of spectral
 sensitivity curve in MSPA program * Right: Weighting on right side of
 spectral sensitivity curve in MSPA program * Baseline: Wavelength where
 relative optical density is set to 0. * Normalize: Wavelength where
 relative optical density is set to 1 (maximum within spectral sensitivity
 curve) * GA1_lambda: The lambda max when the curve was fitted to an A1
 chromophore visual pigment based on Govardovskii et al. (2000) template *
 GA1_fit: Goodness of fit of the data to the A1 template (0-1) *
 GA2_lambda: The lambda max when the curve was fitted to an A2 chromophore
 visual pigment based on Govardovskii et al. (2000) template * GA2_fit:
 Goodness of fit of the data to the A2 template (0-1) * Best_Fit: denotes
 whether an A1 or an A2 chromophore showed the best fit with the spectral
 sensitivity template * Comments: notes two scans of photoreceptors that
 were then bleached and re-scanned with bleach scans available in the raw
 data (bleached photoreceptors are not included in the MSP summary data).
 **2. *H tuberculatus* raw MSP scan data and MSPA program outputs** This
 folder contains raw MSP scan data and MSPA program outputs (files ending
 in -A) for two specimens of *Hyperolius tuberculatus*, which are
 summarized in the file ‘Htuberculatus_msp.csv’ Each specimen is separated
 into a separate folder  labeled with “Field number_genus_species_sex”.
 Within each specimen folder, raw scans are organized into folders
 according to the type of photoreceptor scanned. These include: green
 cones, yellow cones, green rods, red rods. Each scanned photoreceptor
 produces two files with identical names and different extensions - a JPG
 file showing a plot of the raw scan data, mean (black line) and template
 fits (colored lines), and an XLS file showing raw data for the scan. These
 XLS files can be opened in excel or in a text editor.  In each raw data
 file, the first row is blank. The second row has headers and the third row
 input for identifying the specimen and cell the scan belongs to. These
 include: species, common name, age (AD = adult, TAD = tadpole, SUB =
 subadult), Prep# (retinal preparation number from the specimen), Specimen#
 (specimen number from the species, here generally 1), Class (area of the
 spectrum with peak sensitivity; B = blue, G = green, Y = yellow, R = red),
 Cell Type (R = rod, C = cone). The fourth row contains headers for the
 data, and all following rows contain data. Wavelength is in nanometers.
 Baseline and signal are used to normalize the scan. Absorbance gives raw
 absorbance values. NormalizeABS gives normalized absorbance. Curve fit
 shows smoothed normalized absorbance data. The MSPA output files (those
 ending with -A) include a .JPG depicting the fitted curves and a .XLS with
 the fitted curve values for the A1 and A2 chromophore visual pigment based
 on Govardovskii et al. (2000) template #### File: Reflectance.zip
 **Description:** Reflectance measurements of *Hyperolius* *tuberculatus*
 frogs and the foliage substrates they were found on. Data are organized by
 experimental setting. WildFrogs are measurements taken at the field site.
 LabFrogs are measurements taken for the hormone exposure experiment in the
 laboratory. The first column is the wavelength and the second column is
 the reflectance. Files are named
 "fieldnumber.subject.sex.color.replicate" such that
 RCB305.frog.F.O.A.txt corresponds to the reflectance of field sample
 RCB305, frog, female, orange, replicate A. R code to analyze reflectance
 data as implemented in *pavo*. #### File: VisualModeling.zip
 **Description:** R code and custom visual models (Bird_rod, Dog_rod,
 Frog_rod_template, Snake_cone) as implemented in pavo. Frogs+Plants are
 the representative frog and foliage measurements used in the visual
 modeling analyses. For custom visual models, wl refers to wavelength and
 the subsequent column(s) are the templates fitted to the peak absorption
 (λmax) for the corresponding photoreceptor.