Data from: Evidence for ecological tuning of anuran biofluorescent signals
Abstract
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.
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