Date: 18 December, 2023

Dataset Title: Body size and predator cues structure variation in defensive displays of Neotropical calico snakes (Oxyrhopus spp.)

Dataset Creators: Briana A. Sealey*,  Joanna G. Larson*,  Erin P. Westeen, Ciara M. Sánchez-Paredes, Talia Y. Moore,  Alison R. Davis Rabosky
*Authors contributed equally

Dataset Contact: Joanna G. Larson (jglarson@umich.edu)

Funding: Packard Foundation and University of Michigan

Key Points:
-We experimentally tested for the effects of four simulated predator cues on defensive displays in two species of South American calico snakes (genus Oxyrhopus).
-We found that juvenile snakes were both more likely to respond and to respond more strongly than adults and that displays were most common in response to tactile stimuli than to other treatments. 

Research Overview:
In this study, we experimentally tested for the effects of four simulated predator cues on defensive displays in two species of South American calico snakes (genus Oxyrhopus). We found that juvenile snakes were both more likely to respond and to respond more strongly than adults and that displays were most common in response to tactile stimuli than to other treatments. However, we also found broad similarity across both simulated predator treatments and species in the components used in each snake’s defensive display, suggesting a high degree of stereotyping. This research suggests an important role for both ontogeny and intensity of predation risk in structuring variation in defensive behavior in Neotropical snakes and emphasizes the foundational importance of context dependence in conceptual frameworks for understanding predator-prey interactions.

Methodology:
All animal-related procedures have been approved by the University of Michigan Institutional Animal Care and Use Committee (Protocols #PRO00006234 and #PRO00008306) and the Peruvian government SERFOR (Servicio Nacional Forestal y de Fauna Silvestre; permit numbers: 029-2016-SERFOR-DGGSPFFS, 405-2016-SERFOR-DGGSPFFS, 116-2017-SERFOR-DGGSPFFS). We collected data from 31 individuals of Oxyrhopus melanogenys and O. petolarius across a wide range of body sizes from Los Amigos Biological Station in the Madre de Dios region of Peru in November 2016, November 2017, and November 2018, and from Villa Carmen Research Station in the Cusco region of Peru in October 2016.  We performed all behavioral trials in a standardized portable field arena (55cm x 173cm x 61cm) and filmed with two overhead view cameras and one lateral view camera that were GoPro Hero4+ Black or Hero5+ Black.  We exposed snakes to four different treatment types in a randomized order to simulate different predator encounters: pulsed vibration, white overhead looming cue, black overhead looming cue, and tactile stimulus.  For each treatment, we exposed the snake to the stimulus for up to 1 minute, with 1 minute rest periods in between trials. We used QuickTime Player 7 to watch videos frame-by-frame and score anti-predator defensive behaviors following the framework described in Davis Rabosky et al. 2021 (http://dx.doi.org/10.1093/biolinnean/blaa222). This modular approach characterizes snake behavior separately by functional region, thereby capturing any decoupled changes between the head and neck, body, and tail. For each body region, we evaluated behaviors in five categories: Shape, Presentation, Position, Posture, and Movement. We wrote code in R v4.2.3 to analyze and compare the ethograms.

Required R packages to run the code:
plotrix
lme4
scales
lmerTest
raster
MatrixCorrelation
RColorBrewer
devtools
nationalparkscolors

Files contained here:

-“Supplementary_material.pdf” has eight figures that are supplementary to the published article. Figures S4-S8 can be generated with the provided code and data. Figures S1-S3 include drawings that correspond to each of the behavioral states used in the analysis of the videos and generation of the ethograms.

-Zipped file “csvs_final” contains 105 .csv files that include the ethograms generated for the analyses included in our study. Files are named with prefixes that denote the time at which the video was captured, the species of the animal, and the stimulus. Some additionally contain the camera angle and the identity of the scorer.  YYYYMMDD-HHMM-GenusspeciesStimulus-[gCamera]-[Initials of Scorer].csv. 

-Zipped file “DataVideos” contains 230 .mpv files corresponding to the 105 trials analyzed for this study. Files are named with prefixes that denote the time at which the video was captured, the species of the animal, the stimulus, and the camera angle. YYYYMMDD-HHMM-GenusspeciesStimulus-gCamera.mpv. For each trial, there will be 1 to 3 video files, depending on how many cameras filmed the trial. Videos of the same trial will have identical file names except for the camera angle designation.

-Zipped file “Figure2” contains three files used to generate Figure 2 and related analyses. The file “Figure2_treatmentSVL_revisions.R” contains the necessary R code. Information on snake individuals used in the study and used in these analyses is included in “svl_match_ADR.txt”. The file “treatment_order_revisions.csv” is the order in which stimuli were presented to individual snakes and is called by the R code to test for the presence of order effects. The code will also call the .csv files stored in the “csvs_final” file, so it should be unzipped prior to running this code.

-Zipped file “PCAFigures” contains 7 files needed to generate Figure 3, Figure S6 and Figure S7 and perform related analyses. There are three .R files that contain the code to generate Figure 3, Figure S6, and Figure S7, respectively. The files “head_key_042019.txt,” “bodies_key_042019.txt,” “tails_key_042019.txt” provide the possible states for the head, body, and tail regions respectively and are called by the R code. The file “response_70.csv” is used by the code to discriminate between snakes that respond to the stimuli and those that did not. The code will also call the .csv files stored in the “csvs_final” file, so it should be unzipped prior to running this code.

-Zipped file “HeatmapFigures” contains the files needed to generate Figures 4, S4, S5, and S8. The files “head_key_042019.txt,” “bodies_key_042019.txt,” “tails_key_042019.txt” provide the possible states for the head, body, and tail regions respectively and are called by the R code. The file “response_70.csv” is used by the code to discriminate between snakes that respond to the stimuli and those that did not. The code will also call the .csv files stored in the “csvs_final” file, so it should be unzipped prior to running this code. The subfolder “heatmaps” contains two additional subfolders, “figures” and “matrices” that contain heatmaps and correlation matrices, respectively, for each body part of each snake individual. The matrices document the correlation between behavioral states in different behavioral categories and the figures are visualizations of the matrices. These files can be generated using “IndividualHeatmaps_matrices.R.”  The correlation matrices will be used by  the R scripts “Figure4_S5_averagedHeatmaps_treatment.R” and “FigureS4_S8_averagedHeatmaps.R.” 

*On January 4, 2024, “Supplementary_material.pdf” was replaced with an updated version that has slightly different versions of Figures S4 and S8 after an error in code was corrected. Within “HeatmapFigures.zip,” two code files, “IndividualHeatmaps_matrices.R” and “FigureS4_S8_averagedHeatmaps.R” were updated to correct the code error.  Three additional files were added to both the “figures” and “matrices” folders within the subfolder “heatmaps.” These files represent the correlation matrices, by body part, and graphical representation of the matrices for one experimental trial that had previously been excluded due to the code error.

Related publication(s):
Sealey, B.A.*, Larson, J.G.*, Westeen, E.P., Sanchez-Paredes, C.M., Moore, T.Y., Davis Rabosky, A.R. Body size and predator cues structure variation in defensive displays of Neotropical calico snakes (Oxyrhopus spp.). Ethology. In press. *Authors contributed equally

Use and Access:

To Cite Data:
Sealey, B. A., Larson, J. G., Westeen, E. P., Sánchez-Paredes, C. M., Moore, T. Y., Davis Rabosky, A. R. Body size and predator cues structure variation in defensive displays of Neotropical calico snakes (Oxyrhopus spp.) [Data set], University of Michigan - Deep Blue Data.