Work Description

Title: Ecological drivers of ultraviolet colour evolution in snakes. Open Access Deposited

h
Attribute Value
Methodology
  • Field collection:: We captured 438 snakes from field expeditions to Peru (2016-2018), Nicaragua (2018), Belize (2019), and the United States (Texas, Colorado; 2021). We collected snakes through a combination of opportunistic foot surveys, pitfall traps, funnel traps, and driving surveys following the protocol of Davis Rabosky et al. (2021). All field methods were approved by Institutional Animal Care and Use Committees (University of Michigan #PRO00006234 and #PRO00008306, Dickinson College #895) and respective governmental authorities (Peru: Servicio Nacional Forestal y de Fauna Silvestre 029-2016-SERFOR-DGGSPFFS, 405-2016-SERFOR-DGGSPFFS, 116-2017-SERFOR-DGGSPFFS; Nicaragua: Ministerio del Ambiente y los Recursos Naturales DGB-IC-058-2017, DGPNB-IC-019-2018, DGPNB- IC-020-2018, DGPNB-IC-002-2019; Belize: Forest Department of the Ministry of Agriculture, Fisheries, Forestry, the Environment and Sustainable Development FD/WL/1/19(10); Texas Parks and Wildlife, #SPR-1020-175; Colorado Department of Natural Resources, #1950298916).

  • Photography:: To quantify reflectance at both visible and UV wavelengths, we used a Nikon D7000 DSLR camera (Nikon Inc., Melville, NY, USA) with full-spectrum conversion (LifePixel; Mukilteo, USA) and equipped with a Coastal Optics UV-VIS-IR 60 mm F/4 macro lens (Jenoptik Optical Systems, Jupiter, FL, USA). We photographed dorsal and ventral surfaces of each specimen with both a Baader (Mammendorf, Germany) UV/IR cut filter and a UV-Pass filter in a standardized setting at each field site with variable F-stops, shutter speeds, and ISO. We illuminated each specimen using both standard incandescent and UVB light bulbs (Reptizoo; Miami, USA) or natural ambient light when electrical power was unavailable in remote locations. We photographed specimens against a blue, black, or white matte background (Hengming; Guangzhou, China) with a 40% gray reflectance standard (Labsphere; North Sutton, USA) and an X-rite color checker passport (Grand Rapids, USA). We performed spectrometry measurements on a subset of snakes from a series of patches representing each unique color on a given snake using an Ocean Insight Flame Miniature Spectrometer (Model: FLAME-S-UV-VIS ES) with a PX-2 Pulsed Xenon Light Source and QR400-7-SR Light Source cable (Ocean Insight; Orlando, USA) calibrated using a Labsphere 99% white reflectance standard (Labsphere; USA).

  • Ecological characterization:: We used primary literature to characterize primary habitat and diel activity patterns for snakes. We assigned species as arboreal following, fossorial following, or aquatic following, and remaining species as terrestrial with quality control via our field surveys above. We assigned diel activity states as diurnal or nocturnal peer-reviewed literature and available field guides (Data S2). Eight species were not assigned a primary diel activity pattern due to lack of available information. We assigned sex using a combination of probes and observations of everted hemipenes in males or by palpating developing offspring in females. We determined age classes (juvenile, adult) by ranking measured snout-vent lengths (SVL) within species to calculate sex-specific size at maturity thresholds for each species or from published literature.
Description
  • Ultraviolet (UV) wavelengths invisible to humans are primarily studied in the context of reproduction and social signaling. This narrow focus can arise from bias in taxa studied, which are often brightly colored in human-visible wavelengths. Our research describes undocumented UV color patterns across 110 diverse species of Western Hemisphere snakes and tests the hypothesized roles of reproduction versus predator avoidance in the evolution of UV coloration. Phylogenetically-informed tests of life stage, sex, and habitat showed unexpected support for the predator defense hypothesis, with pronounced differences in snake conspicuousness explained by UV coloration. UV reflectance was not predictable from any aspect of visible color pattern, suggesting high potential for transformative discoveries in other “cryptically-colored” lineages across the tree of life.
Creator
Depositor
  • hlcrowel@umich.edu
Contact information
Discipline
Funding agency
  • Other Funding Agency
Other Funding agency
  • University of Michigan
Keyword
Citations to related material
  • Crowell, H. L., Curlis, J. D., Weller, H. I., & Davis Rabosky, A. R. (2024). Ecological drivers of ultraviolet colour evolution in snakes. Nature Communications, 15(1), 5213. http://doi.org/10.1038/s41467-024-49506-4
Resource type
Curation notes
  • 2024-07-16: pacerda added updated citation and UV_literature_review.csv which was not originally uploaded.
Last modified
  • 07/16/2024
Published
  • 02/15/2023
Language
DOI
  • https://doi.org/10.7302/2ktf-6k49
License
To Cite this Work:
Crowell, H. L. .., Curlis, J. D., Weller, H. I., Davis Rabosky, A. R. (2023). Ecological drivers of ultraviolet colour evolution in snakes [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/2ktf-6k49

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Files (Count: 13; Size: 33.3 GB)

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

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