Work Description

Title: Ecological drivers of ultraviolet colour evolution in snakes **(updated Jan-5-2024)

Authors: Hayley L. Crowell, John David Curlis, Hannah I. Weller, Alison R. Davis Rabosky

Dataset contact: Alison Davis Rabosky (ardr@umich.edu)

** Funding: University of Michigan

Key Points:
- We document ultraviolet (UV) coloration in snakes for the first time
- Both habitat and diel activity are predictors of UV coloration in snakes
- UV coloration appears to be driven by ecology rather than sexual selection, unlike other squamates
- A large proportion of snake conspicuousness to predators can be attributed to the presence of UV coloration alone

***Summary of Jan-5-2024 Updates***
- all versions of "collated_metrics_final.csv" in each folder has been updated to reflect a previous data entry error correction
- new cone-catch data has been added to several folders to reflect the addition of two new receivers (peafowls and geckos) and the removal of owls from receiver analyses
- R scripts for the adjusted Figure 3 (in Age_sex_models) and added a new Chi-square analysis of UV and visible color correlation
- A new folder for the UV literature review and associated Figure (1) have been added)

Files:

UV_Snakes_Photo_ledger.csv - spreadsheet containing information about which snake photos/specimens were use for which analyses

Folders:

Age_sex_models **(updated Jan-5-2024)
- age_sex_models.R **(updated Jan-5-2024 to include code for new version of Fig. 3) – R script containing all statistical models for analyzing snake age and sex data as related to ultraviolet (UV) color
- collated_metrics_final.csv – all morphometric, capture, and color data associated with 438 individual snakes, used in above R script
- Fig_3.R **(added to folder Jan-5-2024) - code for generating Figure 3 tree and box plots
- species_ecol.csv **(added to folder Jan-5-2024, needed to generate new version of Fig. 3) - spreadsheet of habitat and diel activity scores for each snake species in the pruned tonini phylogenetic tree
- tree_cleaning_zaher_final.csv **(added to folder Jan-5-2024, needed to generate new version of Fig. 3) - spreadsheet containing secondary pruned tree with intergeneric tip substitutions used for additionally testing
of habitat and diel activity analyses in the supplementary material of the associated manuscript
- tonini.csv & tonini.tre **(added to folder Jan-5-2024, needed to generate new version of Fig. 3) - base files needed to build phylogenetic tree that includes the largest number of species from our dataset

Body_region_analyses **(name changed from "Patch_analysis
- collated_metrics_final.csv - all morphometric, capture, and color data associated with 438 individual snakes, used in below R script
- dorsal_ventral_bodyregion.R - **(updated Jan-8-2024 for clearer analyses descriptions) R script used to analyze distribution of UV color across snake body regions

Chi-square_analyses_Fig_S4B **(added Jan-8-2024)
- chisq_revisions.R - runs Chi-squared analyses and creates Fig.S4b
- chisq_table.csv - summary of visible snake colors that reflect UV

Cone_catch_output_csvs **(updated Jan-5-2024 to include new Peafowl and Gecko LEIA files; owl LEIA files removed)
- Local edge intensity analysis (LEIA) output files generated from predator cone catch models, used to calculate snake conspicuousness

Cone_catch_receiver_parameter_csvs **(updated Jan-5-2024 to include new Peafowl files; owl files removed; all files replaced with updated values)
- text files of spectral wavelength sensitivities for six animal receivers (Bluetit, Peafowl, Dog, Human, Gecko, Snake), used for cone-catch analyses

Mspecs_and_zips
- multispectral image (mspec) files and associated zipped folders containing photo scale bars and masks (rois), used for computer-generated UV color metrics and cone-catch analyses

Phylo_ecol_models **(updated Jan-8-2024)
- collated_metrics_final.com - all morphometric, capture, and color data associated with 438 individual snakes, used in below R script
- Phylo_ecol_models.R ** (updated Jan-8-2024 to include new paper title) - R script containing code used to build phylogenetic trees and statistical models used to analyze UV data as it relates
to snake habitat type and diel activity
- species_ecol.csv - spreadsheet of habitat and diel activity scores for each snake species in the pruned tonini phylogenetic tree
- tonini.csv & tonini.tre - base files needed to build phylogenetic tree that includes the largest number of species from our dataset
- tree_cleaning_tonini.final.csv - spreadsheet containing final pruned tree with intergeneric tip substitutions used for habitat and diel
activity analyses
- tree_cleaning_zaher_final.csv - spreadsheet containing secondary pruned tree with intergeneric tip substitutions used for additionally testing
of habitat and diel activity analyses in the supplementary material of the associated manuscript
- zaher.txt - base file needed to build secondary phylogenetic tree for additional phylogenetic analyses as described in the manuscript supplementary material

Raw_data_csvs
- collated_metrics_final.csv - all morphometric, capture, and color data associated with 438 individual snakes, used in below R script
- species_ecol.csv - spreadsheet of habitat and diel activity scores for each snake species in the pruned tonini phylogenetic tree

Receiver_comparisions **(added Jan-8-2024)
- compiled_receiever_metrics.csv - LEIA analysis output for each receiver for each snake
- collated_metrics_final.csv - all morphometric, capture, and color data associated with 438 individual snakes, used in below R script
- Fig_S8.R - code to create Fig.S8 and run receiver pairwise analyses

Snake_photos
- computer_scored_and_QCPA - all raw snake photos used for calculating the computer-scored UV metric and quantitative color pattern analyses (QCPA)
- human_scored - all raw snake photos used for calculating the human-scored UV metric
- patch_analysis - all raw snake photos used for measuring five color-channel reflectances as visualized in Figure 2C in main manuscript

Spec_data_csvs_code
- spec_data_2021.R - code used to smooth and generate supplemental Figure S2
- all spectrometer data associated with the above code and snakes pictured in Figure S2

UV_literature_review **(added Jan-5-2024 - contains all files associated with new Fig.1 and analyses)
- arcspider.R - dependency function that creates Fig. 1, needed to run Fig_1.R code
- Figure_1.R - creates Fig. 1 spider plots
- species_richness_all.csv - total number of species for each taxonomic group included in Fig.1a
- species_richness_verts.csv - total number of species for each vertebrate taxonomic group included in Fig.1b
- uv_lit_review_final.csv **(added Jan-5-2024) - all articles and associated data used for UV color function literature review in Fig 1

Key to CSV Column Headers:

field_ID - identifying number give to each snake in the field
museum_collection - museum where the snake (if vouchered) was deposited (UMMZ = University of Michigan Museum of Zoology, MUSM = Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos)
museum_no - Voucher number assigned by museum collection where snake is housed
clade - taxonomic clade, family or subfamily
genus
species
country
year
svl - snout-vent length (standard length measurement for snakes) in mm
mass - in grams
consensus_age - age class of snake as determined independently by two or more authors
consensus_sex - sex of snake as determined by two or more authors
gravid - were developing eggs or follicles detected via palpation

Color scoring headers:
vis_color(1-4)_dorsal - up to four visible dorsal colors were scored for each specimen, NAs represent snakes with less than four visible colors
vis_color(1-4)_ventral - up to four visible ventral colors were scored for each specimen, NAs represent snakes with less than four visible colors
uv_color(1-3)_dorsal - up to four uv-reflecting dorsal colors were scored for each specimen, NAs represent snakes with less than four uv-reflecting colors
uv_color(1-3)_ventral - up to four uv-reflecting ventral colors were scored for each specimen, NAs represent snakes with less than four uv-reflecting colors
uv_presence_overall - Y or N, whether the snake had uv-reflecting color anywhere on its body
uv_presence_dorsal - Y or N, whether the snake had uv-reflecting color anywhere on the dorsal surface of its body
uv_dorsal_region - portion of the snake (head,body,tail) that reflected uv color on its dorsal surface
uv_presence_ventral - Y or N, whether the snake had uv-reflecting color anywhere on the ventral surface of its body
uv_ventral_region - portion of the snake (head,body,tail) that reflected uv color on its ventral surface
dorsalcov_mean - average percentage of dorsal surface of snake reflecting uv (as determined by two independent observers)
ventralcov_mean - average percentage of ventral surface of snake reflecting uv (as determined by two independent observers)
dorsal_uv_brightness - average percent brightness of dorsal uv reflectance relative to 40% color standard in photo (as determined by two independent observers)
ventral_uv_brightness - average percent brightness of ventral uv reflectance relative to 40% color standard in photo (as determined by two independent observers)

gen_sp - genus and species of snake repeated for quick reference and coding purposes

bright_cov_dorsal - human-scored metric for dorsal uv reflectance
bright_cov_ventral - human-scored metric for ventral uv reflectance
bright_cov_overall - human-scored metric for overall uv reflectance
Metric_ventral - computer-scored metric for ventral uv reflectance
Metric_dorsal - computer-scored metric for dorsal uv reflectance

diel - daily activity pattern for each species, determined as either nocturnal or diurnal (NA means activity data is unavailable for that species)
ecology_primary - the primary habitat type for each species

** blank spaces and 0 denote colors that could not be determined either due to photo exposure problems or because photo of that snake surface was not taken, respectively

Related Publications:
Crowell, H.L. et al. (2024). Ecological drivers of ultraviolet colour evolution in snakes. Forthcoming

Use and Access:
This data is made available under Attribution-NonCommerical 4.0 International license CC BY-NC 4.0.

To Cite Data:
Crowell, H.L., Curlis, J.D., Weller, H.I., & Davis Rabosky, A.R. (2024). Ecological drivers of ultraviolet colour evolution in snakes [Dataset]. University of Michigan - Deep Blue. http://doi.org/10.7302/2ktf-6k49