https://doi.org/10.5061/dryad.rv15dv4f7

This data set contains all the original files used in our manuscript. Despite the increasing number of studies on natural photonic structures, we seldom know the biological relevance or ecological drivers of these structures. In this study, we used a macroecological approach to look for potential ecological drivers of unique optical effects in 261 specimens representing 46 species of Australian scarabs, known as Christmas beetles (Scarabaeidae: Rutelinae).

This set contains the raw values of reflectance and transmittance measured with spectrometry techniques. As well as the correspondent reflectivity, transmissivity, and absorptivity (integrated across the wavelength range of the solar irradiance). In addition, it contains the raw RGB values extracted from calibrated photographs and used to calculate polarization parameters, as well as the standardization parameters needed to linearize and equalize these RGB values making them comparable across all photographs. These two sets correspond to the characterization of the optical properties of the beetle elytra.

This set also contains the Climate and vegetation data collected from Atlas of Living Australia and the Australian Gridded Climate Data (AGCD)/AWAP database (Australian Bureau of Meteorology official dataset for monthly gridded rainfall analysis). These were extracted for the precise locations of our specimens and the months corresponding to the activity period of each species. We also collected the length of each species as a proxy of size.

Finally, to explore the correlations between the optical properties and climate while controlling by phylogenetic relatedness, we also assembled a phylogenetic tree with published COI data and NCBI sequences. The results of the phylogenetic reconstruction are also included in this data set.

This ReadMe file was generated on 2023-11-10 by Laura Bibiana Ospina-Rozo. Data was collected between 2019 to 2022 in Melbourne Australia.

Description of the data and file structure

File List:

• ParametersMatLab - 15 text files obtained by our MATLAB linearization and equalization tool. Since they all have the same format, we describe one example below. Their name follows the format: "StandardParamsF01LCP", StandardParams + three characters ( in this case F01) referring to the camera configuration + three characters (LCP) referring to the filter, i.e., visible, left-handed polarized or right-handed polarized
• 1_Reflectance_HRBatch.csv - Raw reflectance profile of the subset of individuals from the Pretty Cool Beetles manuscript
• 2_Reflectance_FirstBatch.csv - Raw reflectance profile from the rest of the individuals
• 3_Transmittance_HRBatch.csv - Raw transmittance profile of the subset of individuals from the Pretty Cool Beetles manuscript
• 4_SunIrradiance.csv - Spectral profile correspondent to the sun irradiance
• 5_Locations.csv - Includes location data from each beetle specimen and their activity periods
• 6_VegetationVariables.csv - Vegetation variables extracted by our code from Atlas of Living Australia
• 7_ClimateVariables.csv - Climate variables extracted from continent-wide 0.05° grids of interpolated weather data from the Australian Gridded Climate Data (AGCD)/AWAP database (Australian Bureau of Meteorology official dataset for monthly gridded rainfall analysis)
• 8_Size.csv - Sice of each specimen in cm
• 9_CodesAndSpecies.csv - Species names for each of the code names used in the other files
• 10_Polarization.csv - RGB values extracted from the calibrated photographs under three different filters: VIS, LCP (left polarized) and RCP (right polarized)
• 12_knownGreyStdReflectance.csv - Reflectance of the grey standard under each filter provided by the fabricant. We used the same value for the three of them since all photographs were taken with the lens in the visible spectral range
• 13_SuppTransmittancvsAbsorbance.csv - Transmitivity and absorptivity in visible light for the subset of beetles studied in "Pretty Cool Beetles"
• ConsReflEcolSpp.csv - Consolidated file with the reflectivity values for each spectral band, the PC components (summarizing ecological variables), and size
• SupplementaryBeetleDataBase.csv - Table including the species names and ANIC references for the samples used, when available. This is also available in the interactive version of the code
• SupplementaryBeetleDataBase.xlsx - same as the previous file in .xlsx format
• XMAS_mat2b_bst2e.xml - The BEAST xml file for generating phylogenetic trees from the Christmas beetle supermatrix data. Includes the sequence data, partition evolution model, and various prior topological and dating age constraints.
• xmas_mat2b_bst2ef_set23nn2_pinct_med.tre - Maximum clade credibility consensus of the tree set, made by TreeAnnotator. Includes node posterior support, age confidence interval, and branch rate information.
• XMAS_mat2b_bst2ef_set23nn2_pinct.nwk - The set of 2000 trees randomly drawn from the BEAST posterior sample, is used for comparative analysis. These have been pruned back to the focal taxa, had tip increment added and labels revised to match the trait dataset.

Specific information by file (includes variable names and abbreviations)

Parameters MatLab\StandardParamsF01LCP.txt (only one example since they are all in the same format)

Number of columns: 9

Number of cases/rows: 5

Variable List:

• a, b, c, and d are the parameters needed in the linearization/equalization equations.
  adjR2 is the correlation coefficient for each fitting done by MatLab. These values should always be around 0.99
  seq is just a list of numbers
• Channel is the channel of the photograph, red, green, blue, and gray average value.
• The photograph contains the code of the photograph used for this standardization

1_Reflectance_HRBatch.csv

Number of cols: 57

Number of cases/rows: 1302

Variable List:

• The first column (wl) is the wavelength and all the other columns are the reflectance (% in comparison to a white standard) for each beetle species

Missing data codes: no

Specialized formats or other abbreviations used: All the species abbreviations are detailed in the file 9_CodesAndSpecies.csv

2_Reflectance_FirstBatch

Number of variables: 237

Number of cases/rows: 901

Variable List:

• The first column (wl) is the wavelength and all the other columns are the reflectance (% in comparison to a white standard) for each beetle species

Missing data codes: no

Specialized formats or other abbreviations used: All the species abbreviations are detailed in the file 9_CodesAndSpecies.csv

3_Transmittance_HRBatch

Number of variables: 57

Number of cases/rows: 701

Variable List:

• The first column (wl) is the wavelength and all the other columns are the transmittance (% in comparison to the full beam of light captured by the detector) for each beetle species

Missing data codes: no

Specialized formats or other abbreviations used: All the species abbreviations are detailed in the file 9_CodesAndSpecies.csv

4_SunIrradiance

Number of variables: 2

Number of cases/rows: 852

Variable List:

• The first column (wl) is the wavelength and column 2 is the sun irradiance

5_Locations

Number of variables: 9

Number of cases/rows: 277

Variable List:

• Spp - Specimen code
• Reg - ANIC reference if available, otherwise the code of the polarization photo for ID purposes.
• Latitude - location
• Longitude - location
• MonthMaxALA - month with maximum ALA records for each species
• MonthCollectionLabel - the month when each specimen was collected
• MonthsActivityALA - For each species, we calculated the percentage of records for each month relative to the total, and only considered the months with several records equivalent to >10% of total records for the species.
• Batch - HR means this beetle was also studied in the manuscript "Pretty cool beetles". Beetles labeled "original" in this column were studied only in this manuscript.
• NameinHR - for specimens studied in "Pretty Cool Beetles" the codes used in that manuscript are provided for ID purposes.

Missing data codes: no

Specialized formats or other abbreviations used: All the species abbreviations are detailed in the file 9_CodesAndSpecies.csv

6_VegetationVariables

Number of columns: 18

Number of cases/rows: 277

Variable List:

• spp - beetle specimen code
• reg - ANIC reference if available, otherwise the code of the polarization photo for ID purposes.
• Latitude - location
• Longitude - location
• ALA.month - Month in ALA with most records
• picode - Polarization Photo number for ID purposes
• colection.month - the month when each specimen was collected
• Batch - HR means this beetle was also studied in the manuscript "Pretty cool beetles". beetles labeled "original" in this column were studied only in this manuscript.
• NameinHR - for specimens studied in "Pretty Cool Beetles" the codes used in that manuscript are provided for ID purposes.
• NameinTree - species name as it appears in the phylogenetic tree

The following are the ecological variables related to vegetation cover recovered from ALA:

• NPPMean - Mean annual net primary productivity (tonnes/ha/yr)
• fractionalCoverBareSoil20120305 - Fraction of bare soil
• leafAreaIndexLAI20120305 - leaf area index
• fractionOfPhotosyntheticallyActiveRadiationFPAR - the fraction of photosynthetically active radiation
• aridityIndexAnnualMean - mean annual aridity index (here multiplied by -1 to facilitate its interpretation since it is originally calculated as the monthly ratio of precipitation to potential evaporation)
• growthIndexC3MacrothermPlantsAnnualMean - growth index of C3Macrotherm
• growthIndexC3MesothermPlantsAnnualMean - growth index of C3 Mesotherm
• growthIndexC4MegathermPlantsAnnualMean - growth index of C4 plants

7_ClimateVariables

Number of columns: 19

Number of cases/rows: 276

Variable List:

• species - beetle specimen code
• reg - ANIC reference if available, otherwise the code of the polarization photo for ID purposes.
• lat - Location latitude
• lon - Location longitude

The following correspond to climatic variables from continent-wide 0.05° grids of interpolated weather data from the Australian Gridded Climate Data (AGCD)/AWAP database (Australian Bureau of Meteorology official dataset for monthly gridded rainfall analysis) averaged over 10 years (2010 - 2020) considering only the interval of the activity peak for each species.

• avg_temp_over_35 - the number of extreme temperature days (maximum temperature > 35°C)
• avg_max_temp - daily measurements averaged per month of the average maximum temperature (°C)
• avg_min_temp - average minimum temperature(°C)
• avg_sol - average solar radiation (kJ × m-2 × day-1)
• avg_year_sol - average solar radiation per year
• avg_year_vpr - average vapor pressure per year
• cloud_cover - yearly mean of Cloud coverage (%) calculated from the ratio of observed integrated daily solar radiation to that of a cloudless day
• avg_rr - rainfall (mm/day)
• avg_vpr - monthly mean of the vapor pressure (hPa)
• avg_temp_over_35_Coll
• avg_max_temp_Coll
• avg_min_temp_Coll
• avg_sol_Coll
• avg_rr_Coll
• avg_vpr_Coll

Missing data codes: no

Specialized formats or other abbreviations used: The suffix _Coll means data that was extracted only for the month that the beetle was collected. However, the data used in our analysis is the data for the whole activity period, which can comprise various months depending on the species and it is indicated here by the absence of the _Coll suffix.

8_Size

Number of columns: 2

Number of cases/rows: 276

Variable List:

• ind - beetle specimen code
• size - the length of the beetle in cm.

9_CodesAndSpecies

Number of columns: 2

Number of cases/rows: 276

Variable List:

• ind - beetle specimen code
• phylogeny_name - species name as it is in the phylogenetic tree

Missing data codes: no

Specialized formats or other abbreviations used: none

10_Polarization

Number of columns: 14

Number of cases/rows: 4942

Variable List:

• ind - beetle specimen code
• SpeciesName - species name as it is in the phylogenetic tree
• ANIC - ANIC code
• Pic_code - Number of the calibrated photograph
• Filter - VIS == visible, LCP == left-handed polarized, RCP == right-handed polarized
• tr - region sampled in the photograph. Either the elytron, pronotum, or gray standard.
• label - channel R == red, G == green, B == blue.
• area - sampled area (units are not needed since the photo was not calibrated for size. We selected a small area sample where there is no glare or artifacts)
• mean - mean intensity value - intensity values vary between 0 (absence of light) and 255 (maximum intensity)
• min - min intensity value - intensity values vary between 0 (absence of light) and 255 (maximum intensity)
• max - max intensity value - intensity values vary between 0 (absence of light) and 255 (maximum intensity)
• camera_cat - configuration of the camera. This parameter is necessary because the photos were taken on different days, so there is one set of calibration parameters per day. Each photograph is calibrated according to its corresponding parameters.
• location - RoI == sampled in the region of interest, grey == sampled in the greay standard.
• patch_ID - ID of the patch

12_knownGreyStdReflectance

Number of columns: 2

Number of cases/rows: 3

Variable List:

• 0.38446 is the reflectance of the grey standard included in each photograph. This value is given by the manufacturer. We used the same value for the three filters since the reflectance of the standards varies mostly according to spectral range and all images were taken in visible light.

13_SuppTransmittancvsAbsorbance

Number of columns: 3

Number of cases/rows: 57

Variable List:

• Beetle - beetle specimen code
• Td_VIS - transmissivity (%)
• Ab_VIS - absorptivity (%)
• Original data in "Pretty Cool Beetles"

ConsReflEcolSpp

Number of columns: 8

Number of cases/rows: 48

Variable List:

• the first row is the species name, but it does not contain a header since this is the format required in R for the analysis, i.e., the species name has the be the row label and therefore can not have a header.
• TOT - total reflectivity (broadband 400 to 1700 nm)
• VIS - visible reflectivity (400 to 700 nm)
• NIR - near infrared reflectivity (700 to 1700 nm)
• Res - residuals from the regression between VIS and NIR reflectivity
• PC1 - first principal component summarizing ecological variables
• PC2 - second principal component summarizing ecological variables
• Size - length in cm

SupplementaryBeetleDataBase

Number of columns: 7

Number of cases/rows: 262

Variable List:

• Species_name - species name as it is in the phylogenetic tree
• Code - beetle specimen code
• ANIC reference - ANIC code if available, NA values otherwise.
• Latitude - location for each specimen
• Longitude - location for each specimen
• Batch - HR means this beetle was also studied in the manuscript "Pretty cool beetles". Beetles labeled "original" in this column were studied only in this manuscript.
• NameinHR - for specimens studied in "Pretty Cool Beetles" the codes used in that manuscript are provided for ID purposes. NA values were assigned to species that were not studied in the previous manuscript "Pretty cool beetles".

Missing data codes: NA values in the column ANIC reference if the code is not available. Also, NA values in the column NameinHR for all beetles are labeled "original" in the column "Batch".

Specialized formats or other abbreviations used: NA

Phylogeny Data

Notes from the contents of folder phylogeny (outside of the Data folder, but still part of the R project) https://github.com/lospinarozo/PhotonicRebelsCode/tree/main/Phylogeny

• Note that the names of the files are the same as in this data set.

XMAS_mat2b_bst2e.xml:

• The BEAST xml file for generating phylogenetic trees from the Christmas beetle supermatrix data.
• Includes the sequence data, partition evolution model, and various prior topological and dating age constraints.

XMAS_mat2b_bst2ef_set23nn2_pinct.nwk:

• The set of 2000 trees randomly drawn from the BEAST posterior sample, was used for comparative analysis.
• These have been pruned back to the focal taxa, had tip increment added and labels revised to match the trait dataset.

xmas_mat2b_bst2ef_set23nn2_pinct_med.tre:

• Maximum clade credibility consensus of the tree set, made by TreeAnnotator.
• Includes node posterior support, age confidence interval, and branch rate information.

Sharing/Access information

• This data is used in the publication:

"Photonic rebels: reflectivity and polarization of Christmas beetles are not explained by climate" and should be cited using the correspondent Dryad DOI.

In this experiment, we also used data from our previous publication: "Laura Ospina-Rozo, Jegadesan Subbiah, Ainsley Seago, Devi Stuart-Fox, Pretty Cool Beetles: Can Manipulation of Visible and Near-Infrared Sunlight Prevent Overheating?, Integrative Organismal Biology, Volume 4, Issue 1, 2022, obac036, https://doi.org/10.1093/iob/obac036" The files have been attached to this set again and we have added notes to indicate when the same beetle specimen was used for both publications.

• Links to other publicly accessible locations of the data:

Interactive code: https://lospinarozo.github.io/PhotonicRebelsCode/
Original code and data with version control: https://github.com/lospinarozo/PhotonicRebelsCode

Original data and code from Pretty Cool Beetles: https://github.com/lospinarozo/PrettyCoolBeetlesCodeAndData

Code/Software

Our code is divided in mainly two sections:

• Phylogenetic reconstruction: The text file called PAT_script_v5.sh contains various scripts of bash and R code for assisting in the assembling and checking of genetic sequence data super matrices. The scripts include comment lines detailing use. Some code requires software MAFFT and IQTree.
• Statistical analysis: All our models were run in R Statistical Software v4.1.2 87. To run PGLS models we used the packages ape, caper, picante, and phytools. To run the PGLS model on multiple trees, we used loop functions programmed in R. Given the extent of our statistical analysis, the scripts are separated by topic, and the index script explains the purpose of each of them and how they correlate.