DOI: 10.5061/dryad.wpzgmsbxz
title: Data from: Evidence for ecological tuning of anuran biofluorescent signals

description: Although biologists have described biofluorescence in a diversity of taxa,
 there have been few systematic efforts to document the extent of
 biofluorescence within a taxonomic group or investigate its general
 significance. Through a field survey across South America, we discover and
 document patterns of biofluorescence in tropical amphibians. We more than
 triple the number of anuran species that have been tested for this trait.
 We find evidence for ecological tuning (i.e., the specific adaptation of a
 signal to the environment in which it is received) of the biofluorescent
 signals. For 56.58% of species tested, the fluorescence excitation peak
 matches the wavelengths most abundant at twilight, the light environment
 in which most frogs are active. Additionally, biofluorescence emission
 spans both wavelengths of low availability in twilight and the peak
 sensitivity of green-sensitive rods in the anuran eye, likely increasing
 contrast of this signal for a conspecific receiver. We propose an expanded
 key for testing the ecological significance of biofluorescence in future
 studies, providing potential explanations for the other half of
 fluorescent signals not originally meeting formerly proposed criteria.
 With evidence of tuning to the ecology and sensory systems of frogs, our
 results suggest frog biofluorescence is likely functioning in anuran
 communication.
description: # Data for Evidence for ecological tuning of anuran biofluorescent signals
 --- Supporting material for publication submitted to Nature
 Communications. We conducted tests to assesses the variability of
 amphibian biofluorescence and provide insight into its potential
 ecological significance. This dataset includes R Code and relevant raw
 data for all statistical analyses conducted. The order of the scripts in
 this file, follows the order of analyses run and their presentation in the
 manuscript. All scripts were run utilizing R v4.2.3. ## Description of the
 Data and file structure MainManuscriptScript.R: code for (1) spectrometer
 analysis, (2) Kruskal-Wallis one-way analysis of variance test and
 Pairwise Dunn’s tests for assessing differences in excitation and emission
 of biofluorescence by excitation light source (graphs for Fig. 1, Fig. 3,
 and Supp. Fig. 1 in manuscript), (3) visualization of criterion 4 of
 ecological significance, and (4) visualization of all blue-light-induced
 spectrometer recordings for graph in Fig. 2 of manuscript
 ALLindividmax_dat.csv: input for MainManuscriptScript.R, the maximum
 fluorescent emission recording for each individual under each light source
 MAXindividmax_dat.csv: input for MainManuscriptScript.R, the maximum
 fluorescent emission recording for each individual under any light source
 MAXindividmax_dat_loc.csv: input for MainManuscriptScript.R, the maximum
 fluorescent emission recording for each individual under any light source
 (same file as MAXindividmax_dat.csv above) plus column of
 "Body_Loc_Sum". This added column is a summarized version of the
 specific body locations each spectrometer recording was originally labeled
 with. For easier comparison, the body regions were summarized into the
 following nine groups: cloaca, dorsal (including spectrometer recordings
 with a body location specified from any dorsal pattern), eye, facial
 pattern (including lip, spots under the eye, snout, etc.), flank, inguinal
 region, limb (including forelimbs, thigh, etc.), throat (including vocal
 sac), and ventral (including any ventral pattern).
 MAXindividmax_loc_all.txt: file created in MainManuscriptScript.R, the
 maximum fluorescent emission recording for each individual under each
 light source SPindividmax_dat.csv: file created in MainManuscriptScript.R,
 the maximum fluorescent emission recording for each species (from any
 light source) sumstats_Ex.txt: file created in MainManuscriptScript.R, the
 maximum fluorescent emission recording for each family under each
 excitation light source RandTest.R: code for randomization tests for
 criteria 2 and 3 of ecological significance of biofluorescence Rod and
 Spectra.csv: input for RandTest.R, rod spectra from Yovanovich et al. 2017
 and twilight spectra digitized with permission from Cronin et al. 2014
 Individual_Data.csv: input for RandTest.R, individual metadata (species,
 genera, family, etc. by field number) Individ_em_wv_round_less550.csv:
 input for RandTest.R, "green" emission peak data
 Individ_em_wv_round_greater550.csv: input for RandTest.R,
 "orange" emission peak data ## Additions Post Revisions
 RandTest_UpdatedFromRevisions.R: code for randomization tests for criteria
 1, 2, and 3 of ecological significance of biofluorescence updated post
 revisions. Plots for Figures 4 and 5.
 Individ_em_wv_round_green_eitherpeak.csv: input for
 RandTest_UpdatedFromRevisions.R, "green" emission peak data
 including first and second green peaks from emission data (to account for
 bi-modal emission spectra) Individ_em_wv_round_orange_eitherpeak.csv:
 input for RandTest_UpdatedFromRevisions.R, "orange" emission
 peak data including first and second orange peaks from emission data (to
 account for bi-modal emission spectra) ALLindividmax2_dat_RB.csv: input
 for MainManuscriptScript.R taking into account bi-modal peaks under RB
 excitation. The maximum fluorescent emission recording of the first two
 peaks for each individual under RB (440-460 nm) light source ##
 Phylogenetic Correction Analyses AncStateRec.R: code for Ancestral State
 Estimation of biofluorescent emission intensity by excitation wavelength
 BF_species_NEXUS.nex: input for AncStateRec.R, time calibrated phylogeny
 for all species in the analysis available on and downloaded form
 Timetree.org AvgInt_UV.csv, AvgInt_VI.csv, AvgInt_RB.csv, AvgInt_CY.csv,
 AvgInt_GR.csv: input files for AncStateRec.R, average biofluorescent
 emission intensity by species under each excitation wavelength (UV, VI,
 RB, CY, GR). ``` ##RevBayes scripts and data files: constrained optima
 under Ornstein-Uhlenbeck evolution analyses mcmc_OU_MODIFIED.REV: code for
 constrained optima under Ornstein-Uhlenbeck evolution analyses
 pruned_nexustree_greens.nex, pruned_nexustree_oranges.nex: input files for
 mcmc_OU_MODIFIED.REV, trees pruned from BF_species_NEXUS.nex to included
 species for which we have blue light-induced green and orange fluorescent
 emission data respectively. BF_speciesTrimmed_MaxEmissionGreenSpecies.nex,
 BF_speciesTrimmed_MaxEmissionOrangeSpecies.nex: input files for
 mcmc_OU_MODIFIED.REV, character files of fluorescent emission wavelength
 of blue light-induced green and orange fluorescent emission data
 respectively, averaged by species from
 Individ_em_wv_round_green_eitherpeak.csv and
 Individ_em_wv_round_orange_eitherpeak.csv datafiles respectively. AIC.R:
 code for comparison of average likelihood from RevBayes output files for
 the constrained optima Ornstein-Uhlenbeck evolution models under each
 condition ```