This GARCIA_etal_2022_README.txt file was generated on 2022-02-10 by Natalia C. Garcia GENERAL INFORMATION 1. Title of Dataset: Data for: Sexual dichromatism may not be a good index of sexual or natural selection in the blue cardinalids (Aves: Passeriformes). 2. Author Information A. Corresponding Investigator: Name: Natalia C. García Institution: División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" Email: natigarcia86@gmail.com B. Co-investigator 1 Name: Ana S. Barreira Institution: División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" C. Co-investigator 2 Name: Pablo L. Tubaro Institution: División Ornitología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" 3. Date of data collection: 2012-2015 4. Geographic location of data collection: Data collected from specimens from the Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (Buenos Aires, Argentina), the American Museum of Natural History (New York, NY, USA), the California Academy of Sciences (San Francisco, CA, USA) and the Museum of Vertebrate Zoology, University of California (Berkeley, CA, USA). 5. Information about funding sources that supported the collection of the data: American Museum of Natural History (Frank M. Chapman Memorial Fund, NY, USA) Agencia Nacional de Promoción Científica y Tecnológica (PICT 2015-3560, Argentina) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET PIP 112-201501-00637CO, Argentina). 6. Recommended citation for this dataset: García et al. (2022). Data from: Sexual dichromatism may not be a good index of sexual or natural selection in the blue cardinalids (Aves: Passeriformes). Dryad, Dataset. DATA & FILE OVERVIEW 1. File List: File 1 Name: reflectance_spectra.zip File 1 Description: Zipped folder containing all the raw reflectance spectra data for males and females of the 14 species analyzed. Files are organized in 14 directories corresponding to each species, and each have 2 subdirectories for males ("Machos") and females ("Hembras"). Main directories are named by species scientific name, using first 2 letters of genus + first 2 letters of species. Same code is used in corresponding R scripts. Reflectance spectra files have code names, the link with the specimen ID# from museums is in Table S1 (Supplementary Materials). As an example, in "acc_AMNHm1_p2_a_MALE" acc indicates species/subspecies, AMNH the collection, m1 that was the first male measured for that species/subspecies, p2 is the plumage patch, a is the repetition for that patch and MALE indicates the sex. Plumages patches numbers are as follows: chest (2), belly (3), lower belly (4), forehead (5), crown (6), back (8), rump (9). Same code is used in corresponding R scripts. File 2 Name: 0.get_data.R File 2 Description: R script used to read and process raw reflectance spectra data from "reflectance_spectra.zip". Data is saved as "averaged_smoothed_spectra.Rdata". File 3 Name: averaged_smoothed_spectra.Rdata File 3 Description: Rdata file containing the processed reflectance spectra data obtained after executing "0.get_data.R". File 4 Name: 1.Dichro_UV_bypatches.R File 4 Description: R script used to calculate perceptual distances between males and females’ plumage coloration as a proxy of sexual dichromatism, considering a UV-sensitive visual system. File 5 Name: a.Dichro_V_bypatches.R File 5 Description: R script used to calculate perceptual distances between males and females’ plumage coloration as a proxy of sexual dichromatism, considering a V-sensitive visual system. File 6 Name: 2.color_sum_UV_bypatches.R File 6 Description: R script used to calculate color span as an index of colorfulness, considering a UV-sensitive visual system. File 7 Name: b.color_sum_V_bypatches.R File 7 Description: R script used to calculate color span as an index of colorfulness, considering a V-sensitive visual system. File 8 Name: bkg_vismodel_UV.RData File 8 Description: Absolute quantum catches at each photoreceptor for each background considering a UV-sensitive visual system (original background reflectance spectra were obtained from NASA https://speclib.jpl.nasa.gov/). File 9 Name: bkg_vismodel_V.RData File 9 Description: Absolute quantum catches at each photoreceptor for each background considering a V-sensitive visual system (original background reflectance spectra were obtained from NASA https://speclib.jpl.nasa.gov/). File 10 Name: 3.bkg_male_UV.R File 10 Description: R script used to calculate perceptual distance between bird and vegetated background as a proxy of conspicuousness for males, considering a UV-sensitive visual system. File 11 Name: c.bkg_male_V.R File 11 Description: R script used to calculate perceptual distance between bird and vegetated background as a proxy of conspicuousness for males, considering a V-sensitive visual system. File 12 Name: 4.bkg_female_UV.R File 12 Description: R script used to calculate perceptual distance between bird and vegetated background as a proxy of conspicuousness for females, considering a UV-sensitive visual system. File 13 Name: d.bkg_female_V.R File 13 Description: R script used to calculate perceptual distance between bird and vegetated background as a proxy of conspicuousness for females, considering a V-sensitive visual system. File 14 Name: 5.bkg_dry_male_UV.R File 14 Description: R script used to calculate calculate perceptual distance between bird and nesting background, as a proxy of conspicuousness for males, considering a UV-sensitive visual system. File 15 Name: e.bkg_dry_male_V.R File 15 Description: R script used to calculate calculate perceptual distance between bird and nesting background, as a proxy of conspicuousness for males, considering a V-sensitive visual system. File 16 Name: 6.bkg_dry_female_UV.R File 16 Description: R script used to calculate calculate perceptual distance between bird and nesting background, as a proxy of conspicuousness for females, considering a UV-sensitive visual system. File 17 Name: f.bkg_dry_female_V.R File 17 Description: R script used to calculate calculate perceptual distance between bird and nesting background, as a proxy of conspicuousness for females, considering a V-sensitive visual system. File 18 Name: specimen_age_female.csv File 18 Description: Year of collection and color span (considering a UV-sensitive visual system) estimated for each female specimen. File 19 Name: specimen_age_male.csv File 19 Description: Year of collection and color span (considering a UV-sensitive visual system) estimated for each male specimen. File 20 Name: dicro_colorsum_bkgm_f_drym_f_uv.csv File 20 Description: All variables used to ran phylogenetic-informed tests, considering a UV-sensitive visual system. File obtained after executing R scripts which names start with 1-6. File 21 Name: dicro_colorsum_bkgm_f_drym_f_v.csv File 21 Description: All variables used to ran phylogenetic-informed tests, considering a V-sensitive visual system. File obtained after executing R scripts which names start with a-f. File 22 Name: Tables_S2andS3_Results.R File 22 Description: R script used to ran statistical tests to check that color variables we used are not significantly related to specimen age. File 23 Name: bluecard_multilocus2.NEX File 23 Description: Tree topology used for phylogenetic generalized least squares regressions, based on the species tree reconstructed by Bryson et al. (Journal of Biogeography 41:587–599, 2014) using a multilocus dataset. File 24 Name: Table4_Results.R File 24 Description: R script used to ran phylogenetic paired t-tests between male and female indexes of colorfulness and conspicuousness, considering a UV-sensitive visual system. File 25 Name: TableS9_Results.R File 25 Description: R script used to ran phylogenetic paired t-tests between male and female indexes of colorfulness and conspicuousness, considering a V-sensitive visual system. File 26 Name: Table5_Results.R File 26 Description: R script used to ran phylogenetic generalized least square regression tests, with indexes of male and female colorfulness and conspicuousness as predictors and indexes of sexual dichromatism as dependent variables, considering a UV-sensitive visual system. File 27 Name: TableS10_Results.R File 27 Description: R script used to ran phylogenetic generalized least square regressions tests, with indexes of male and female colorfulness and conspicuousness as predictors and indexes of sexual dichromatism as dependent variables, considering a V-sensitive visual system. 2. Relationship between files, if important: R scripts which names start with 1-6 or a-f need to be executed in order, and can be executed after script 0.get_data.R or loading "averaged_smoothed_spectra.Rdata" R scripts Table4_Results.R and Table5_Results.R require the phylogenetic tree from bluecard_multilocus2.NEX and the .csv table produced after executing scripts which names start with 1-6, "dicro_colorsum_bkgm_f_drym_f_uv.csv". R scripts TableS9_Results.R and TableS10_Results.R require the phylogenetic tree from bluecard_multilocus2.NEX and the .csv table produced after executing scripts scripts which names start with a-f, "dicro_colorsum_bkgm_f_drym_f_v.csv". METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Reflectance spectra for males and females of 14 bird species were obtained from museum skins deposited at four different museums. Plumage reflectance spectra were measured on seven plumage patches (chest, belly, lower belly, forehead, crown, back and rump) three times, replacing the probe each time. Reflectance measurements were taken using an Ocean Optics USB 4000 and an Ocean Optics USB 2000 spectrophotometer, with a PX-2 xenon light source (effective range of emission from 220 to 750 nm) calibrated against a WS-1 diffuse reflectance white standard (Ocean Optics, Inc., Dunedin, Florida, USA). Plumage was illuminated and the reflected light was collected with a bifurcated probe located perpendicularly and approximately 5 -15 mm away from the museum skin surface. The probe was placed on a rubber holder that kept it at a fixed distance from the surface and isolated from ambient light. Each spectrum was the average of 5 readings with an integration time of 100 msec. A boxcar smoothing function of 5 was used, and the equipment was re-calibrated before measuring plumage reflectance on each specimen. 2. Methods for processing the data and software-specific information needed to interpret the data: The package pavo for R v. 4.0.3 was used to import the reflectance spectra data, keep one reflectance value per nm between 300 and 700 nm (reflectance values are interpolated to the nearest wavelength integer), apply a smoothing function (smoothing parameter = 0.2) and replace negative reflectance values (due to equipment noise on low reflectance measurements) with 0. The three readings obtained for each plumage patch were averaged, obtaining a single reflectance spectrum with one reflectance value per nm between 300 and 700 nm for each plumage patch for each specimen. 3. People involved with sample collection, processing, analysis and/or submission: All reflectance measurements were taken by the Corresponding Investigator. DATA-SPECIFIC INFORMATION FOR: specimen_age_female.csv 1. Number of variables: 3 2. Number of cases/rows: 154 3. Variable List: species: code indicating species scientific name, using first 2 letters of genus + first 2 letters of species year: year the specimen was collected colspan.m: color span in arbitrary units 4. Specialized formats or other abbreviations used: amco :Amaurospiza concolor ammo: Amaurospiza Moesta cybr: Cyanoloxia brissonii cycy: Cyanoloxia cyanoides cyro: Cyanoloxia rothschildii cygl: Cyanoloxia glaucocaerulea cypa: Cyanocompsa parellina paam: Passerina amoena paca: Passerina caerulea paci: Passerina iris pacy: Passerina cyanea pale: Passerina leclancherii paro: Passerina rositae pave: Passerina versicolor DATA-SPECIFIC INFORMATION FOR: specimen_age_male.csv 1. Number of variables: 3 2. Number of cases/rows: 187 3. Variable List: species: code indicating species scientific name, using first 2 letters of genus + first 2 letters of species year: year the specimen was collected colspan.m: color span in arbitrary units 4. Specialized formats or other abbreviations used: amco : Amaurospiza concolor ammo: Amaurospiza Moesta cybr: Cyanoloxia brissonii cycy: Cyanoloxia cyanoides cyro: Cyanoloxia rothschildii cygl: Cyanoloxia glaucocaerulea cypa: Cyanocompsa parellina paam: Passerina amoena paca: Passerina caerulea paci: Passerina iris pacy: Passerina cyanea pale: Passerina leclancherii paro: Passerina rositae pave: Passerina versicolor DATA-SPECIFIC INFORMATION FOR: dicro_colorsum_bkgm_f_drym_f_uv.csv 1. Number of variables: 24 2. Number of cases/rows: 14 3. Variable List: species_mean: chromatic perceptual distance (ΔS) between males and females averaged across plumage patches, in JNDs (Just Noticeable Differences). species_max: chromatic perceptual distance (ΔS) between males and females for the plumage patch with maximum value, in JNDs. ventral_dicro_mean: chromatic perceptual distance (ΔS) between males and females averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. dorsal_dicro_mean: chromatic perceptual distance (ΔS) between males and females averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. colspan.f: color span for females, in arbitrary units. colspan.f.SE: color span standard error for females. colspan.m: color span for males, in arbitrary units. colspan.m.SE: color span standard error for females. ventral_mean_males: chromatic perceptual distance (ΔS) between males and vegetated background averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. ventral_max_males: chromatic perceptual distance (ΔS) between males and vegetated background for the ventral plumage patch with maximum value, in JNDs. dorsal_mean_males: chromatic perceptual distance (ΔS) between males and vegetated background averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. dorsal_max_males: chromatic perceptual distance (ΔS) between males and vegetated background for the dorsal plumage patch with maximum value, in JNDs. ventral_mean_females: chromatic perceptual distance (ΔS) between females and vegetated background averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. ventral_max_females: chromatic perceptual distance (ΔS) between females and vegetated background for the ventral plumage patch with maximum value, in JNDs. dorsal_mean_females: chromatic perceptual distance (ΔS) between females and vegetated background averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. dorsal_max_females: chromatic perceptual distance (ΔS) between females and vegetated background for the dorsal plumage patch with maximum value, in JNDs. ventral_dry_mean_males: chromatic perceptual distance (ΔS) between males and nesting background averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. ventral_dry_max_males: chromatic perceptual distance (ΔS) between males and nesting background for the ventral plumage patch with maximum value, in JNDs. dorsal_dry_mean_males: chromatic perceptual distance (ΔS) between males and nesting background averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. dorsal_dry_max_males: chromatic perceptual distance (ΔS) between males and nesting background for the dorsal plumage patch with maximum value, in JNDs. ventral_dry_mean_females: chromatic perceptual distance (ΔS) between females and nesting background averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. ventral_dry_max_females: chromatic perceptual distance (ΔS) between females and nesting background for the ventral plumage patch with maximum value, in JNDs. dorsal_dry_mean_females: chromatic perceptual distance (ΔS) between females and nesting background averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. dorsal_dry_max_females: chromatic perceptual distance (ΔS) between females and nesting background for the dorsal plumage patch with maximum value, in JNDs. 4. Specialized formats or other abbreviations used: amco : Amaurospiza concolor ammo: Amaurospiza Moesta cybr: Cyanoloxia brissonii cycy: Cyanoloxia cyanoides cyro: Cyanoloxia rothschildii cygl: Cyanoloxia glaucocaerulea cypa: Cyanocompsa parellina paam: Passerina amoena paca: Passerina caerulea paci: Passerina iris pacy: Passerina cyanea pale: Passerina leclancherii paro: Passerina rosita pave: Passerina versicolor DATA-SPECIFIC INFORMATION FOR: dicro_colorsum_bkgm_f_drym_f_v.csv 1. Number of variables: 24 2. Number of cases/rows: 14 3. Variable List: species_mean: chromatic perceptual distance (ΔS) between males and females averaged across plumage patches, in JNDs (Just Noticeable Differences). species_max: chromatic perceptual distance (ΔS) between males and females for the plumage patch with maximum value, in JNDs. ventral_dicro_mean: chromatic perceptual distance (ΔS) between males and females averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. dorsal_dicro_mean: chromatic perceptual distance (ΔS) between males and females averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. colspan.f: color span for females, in arbitrary units. colspan.f.SE: color span standard error for females. colspan.m: color span for males, in arbitrary units. colspan.m.SE: color span standard error for females. ventral_mean_males: chromatic perceptual distance (ΔS) between males and vegetated background averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. ventral_max_males: chromatic perceptual distance (ΔS) between males and vegetated background for the ventral plumage patch with maximum value, in JNDs. dorsal_mean_males: chromatic perceptual distance (ΔS) between males and vegetated background averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. dorsal_max_males: chromatic perceptual distance (ΔS) between males and vegetated background for the dorsal plumage patch with maximum value, in JNDs. ventral_mean_females: chromatic perceptual distance (ΔS) between females and vegetated background averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. ventral_max_females: chromatic perceptual distance (ΔS) between females and vegetated background for the ventral plumage patch with maximum value, in JNDs. dorsal_mean_females: chromatic perceptual distance (ΔS) between females and vegetated background averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. dorsal_max_females: chromatic perceptual distance (ΔS) between females and vegetated background for the dorsal plumage patch with maximum value, in JNDs. ventral_dry_mean_males: chromatic perceptual distance (ΔS) between males and nesting background averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. ventral_dry_max_males: chromatic perceptual distance (ΔS) between males and nesting background for the ventral plumage patch with maximum value, in JNDs. dorsal_dry_mean_males: chromatic perceptual distance (ΔS) between males and nesting background averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. dorsal_dry_max_males: chromatic perceptual distance (ΔS) between males and nesting background for the dorsal plumage patch with maximum value, in JNDs. ventral_dry_mean_females: chromatic perceptual distance (ΔS) between females and nesting background averaged across ventral plumage patches (chest, belly, lower belly), in JNDs. ventral_dry_max_females: chromatic perceptual distance (ΔS) between females and nesting background for the ventral plumage patch with maximum value, in JNDs. dorsal_dry_mean_females: chromatic perceptual distance (ΔS) between females and nesting background averaged across dorsal plumage patches (forehead, crown, back, rump), in JNDs. dorsal_dry_max_females: chromatic perceptual distance (ΔS) between females and nesting background for the dorsal plumage patch with maximum value, in JNDs. 4. Specialized formats or other abbreviations used: amco : Amaurospiza concolor ammo: Amaurospiza Moesta cybr: Cyanoloxia brissonii cycy: Cyanoloxia cyanoides cyro: Cyanoloxia rothschildii cygl: Cyanoloxia glaucocaerulea cypa: Cyanocompsa parellina paam: Passerina amoena paca: Passerina caerulea paci: Passerina iris pacy: Passerina cyanea pale: Passerina leclancherii paro: Passerina rositae pave: Passerina versicolor