Data and code from: Chronic wasting disease exposure risk to male cervids during the mating season in a multi-host community
Data files
Sep 29, 2026 version files 1.13 MB
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AllCervidObs.csv
231.67 KB
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BuckBehaviorData.csv
84.06 KB
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CameraLocations_LandownersRemoved.csv
4.69 KB
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cervid.dat.csv
552.44 KB
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CervidInteractions.csv
854 B
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edges_direct_final.csv
745 B
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edges_indirect_final.csv
1.22 KB
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ElkBehaviorData.csv
53.28 KB
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final.dat.csv
7.50 KB
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MultiHostCWDAnalysis_EcologyAndEvolution.R
65.34 KB
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PrevalenceLitReview.csv
108.77 KB
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README.md
16.33 KB
Abstract
Background: Multi-host infectious diseases are challenging to manage due to variation in: 1) spatial overlap amongst species; 2) contact rates; and 3) host competence. Chronic wasting disease, a lethal disease affecting cervids, exemplifies these challenges. The study focuses on three male cervid species (mule deer, white-tailed deer, and elk) during the mating season in an area where CWD is enzootic.
Methods: This study was conducted near Scottsbluff, NE, USA, in the Wildcat Hills. Wildlife camera traps were deployed across three site types, including two potential hotspots for disease transmission - water tanks and white-tailed deer scrape sites - and reference sites that captured background levels of deer activity. Camera traps measured both spatial overlap of male cervid species, along with species-specific contact rates with the environment and conspecifics. Contact rates were used to calculate intra- and interspecific environmental and direct exposure risk under assumptions of both equal and variable competence between species. Variable host competence was evaluated using a systematic review of the scientific literature.
Results and conclusions: Interspecific environmental exposure risk was 100 and 6 times higher at water tank and scrape sites than reference sites for mule deer and white-tailed deer. Risk to elk occurred exclusively at water tanks. All interspecific environmental exposure risk occurred a water tank and scrape sites. Under an assumption of variable competence, the proportion of total risk attributed to intraspecific vs interspecific sources were vastly different when compared to an assumption of equal competence for species with the greatest potential differences in host competence (elk and mule deer). We found no significant differences in direct exposure for mule deer, the only species for which we were able to compare risk across site types.
Dataset DOI: 10.5061/dryad.zpc866tpp
Description of the data and file structure
Study area: Our study area comprised of a mixed-agricultural landscape located to the south of Scottsbluff, NE, USA. Cervid species included elk, mule deer, and white-tailed deer. Bighorn sheep, mountain lions, coyotes, and bobcats also occur in this area.
*Camera trap data: 38 wildlife camera traps were opportunistically deployed at three site types during the cervid mating season: 1) water tanks (n=8); 2) white-tailed deer scrape sites (n=11); and 3) reference sites (n=19). Water tanks were large steel stock tanks used by both cattle and wildlife. White-tailed deer scrape sites were identified by the presence of overhanging lick-branches and bare patches of soil. Reference sites monitored areas of expected or known deer activity (e.g., game trails, edge habitat). Camera traps were active between October 16th 2023 and December 7th 2023, programmed to take 10-second videos with no delay when motion was detected, and each camera trap sampled an approximately 120 m2 area.
This data was used to:
1) Measure duration of contact behaviors: Contact behaviors were recorded using the enclosed ethogram. Environmental contact behaviors resulted in both the uptake and shedding of prions. Direct contact behaviors captured or preceded direct contact between a male cervid and a male or female of the same species. The ethogram was applied to all camera trap videos using Timelapse2 (Greenberg et al., 2019). Only videos containing antlered male mule deer, white-tailed deer, and elk were included. All video clips containing male cervids were consolidated into 1-minute events and coded to extract the contact behaviors of each male cervid. Mean daily duration (sec) of contact behaviors observed in each event were summarized at each camera location for each exposure risk type (environmental/direct). Mean daily durations were calculated by scaling the total number of events to account for camera malfunctions that yielded variable video lengths (mean: 8.19 sec; range: 1-60 sec) and the number of days each camera was operational (mean: 36.4 days; range: 4.2-51.1 days).
2) Estimate probability of spatial overlap of cervid species: Spatial overlap was determined by the co-occurrence of two or more species at a given camera location.
Host Competence: We used differences in CWD prevalence amongst sympatric mule deer, white-tailed deer, and elk as a proxy for variable host competence amongst species. We documented interspecific differences in CWD prevalence via a systematic literature review. To conduct the literature review, we used the Boolean search string: “chronic wasting disease” AND “mule deer” AND “white-tailed deer” AND “elk” AND “prevalence” in Web of Science on March 23rd, 2025. Included studies: 1) calculated or estimated CWD prevalence for free-ranging mule deer, white-tailed deer, and elk in the same study region; 2) in an area where CWD had been present for at least 1 year; and 3) where CWD prevalence was greater than 1% in any of the three species. The search yield 52 studies, and two of these studies met the inclusion criteria (Table 2; see MS).
Exposure Risk: Intraspecific, interspecific, and total environmental exposure risk, along with direct exposure risk, at each site type was calculated using equations outlined in MS to estimated differences for each species and site type. Interspecific exposure risk was also calculated under assumptions of equal and variable host competence across species.
Files and variables
File: MultiHostCWDAnalysis_EcologyAndEvolution.R
Description: Code used to clean, prepare, and analyze data.
File: AllCervidObs.csv
Description: Cervid observations (elk, mule deer, and white-tailed deer) extracted from video data using Timelapse 2 software. Counts of the total number of individuals, number of bucks (males), number of does (females), and number of fawns are included for mule deer and white-tailed deer. See ElkBehaviorData.csv for elk counts.
Variables
- Camera: Unique camera deployed at each site.
- Video: The video in which a cervid was identified at each camera location.
- Obs_ID: Unique observation ID combining site (Camera) and observation (Video).
- DateTime: Date/time stamp of when an observation occurred.
- Species: The species identified in each observation.
- VideoIncompleteCorrupt: A manual flag for corrupted/incomplete videos.
- NumTotalDeer: The total number of deer in each observation.
- NumBucks: The number of bucks in each observation.
- NumDoes: The number of does in each observation.
- NumFawns: The number of fawns in each observation.
- Comments: Observer notes.
File: BuckBehaviorData.csv
Description: Specific behaviors exhibited by individual bucks (mule deer and white-tailed deer) in each observation, along with antler class information and video duration.
Variables
- Camera: Unique camera deployed at each site.
- Video: The video in which a cervid was identified at each camera location.
- Obs_ID: Unique observation ID combining site (Camera) and observation (Video).
- Bin: Cervid group. Deer = Odocoileous spp.
- Behavior1: Behavior exhibited by individual #1 in video.
- Behavior2: Behavior exhibited by individual #2 in video (if >1 individuals)
- Behavior3: Behavior exhibited by individual #3 in video (if >1 individuals)
- Sex1: Sex of individual #1 in video.
- Sex2: Sex of individual #2 in video (if >1 individuals)
- Sex3: Sex of individual #3 in video (if >1 individuals)
- VidDateTime: Date/time stamp of when an observation occurred.
- Antler1: Antler class of individual #1 in video.
- Antler2: Anlter class of individual #2 in video (if >1 individuals)
- Antler3: Anlter class of individual #3 in video (if >1 individuals)
- Sex4: Sex of individual #4 in video (if >1 individuals)
- Antler4: Anlter class of individual #4 in video (if >1 individuals)
- Behavior4: Behavior exhibited by individual #4 in video (if >1 individuals)
- Duration: Video duration.
- MultiBehaviors: Flag for if multiple behaviors occurred in video.
- Comment: Observer notes.
File: CameraLocations_LandownersRemoved.csv
Description:
Variables
- CamNum: Unique camera deployed at each site (site ID).
- Lat: Decimal degrees latitude of camera location.
- Long: Decimal degrees longitude of camera location.
- SetDate: Date camera set.
- FirstImageDateTime: Timestamp of first video.
- LastImageDateTime: Timestamp of last video.
- NumImages: Number of videos.
- ParcelType: Public or private land classification.
- SetType: Site type. Reference sites include High Use and Food Plot. Scrape sites include RubTree sites.
- HabitatBroad: Broad habitat classification (recorded in the field).
- SiteType: Camera located in a wildland or agricultural site.
- DistForest: Distance of camera to nearest forest cover landclass edge (extracted via ArcGIS).
- DistAg: Distance of camera to nearest agricultural land class edge (extracted via ArcGIS).
File: CervidInteractions.csv
Description: Spatial overlap data. The number of observations of each cervid species at each site (CamNum) and a flag for species co-occurrence.
Variables
- CamNum: Unique camera deployed at each site (site ID).
- Deer: Unknown species: Number of observations of Odocoileus spp. at each site.
- MuleDeer: Number of mule deer observations at each site.
- White-tailed: Number of white-tailed deer observations at each site.
- Elk: Number of elk observations at each site.
- NumSpecies: Number of species at each site.
- Interation: Species cooccurence code for each site (M=mule deer, W=white-tailed deer, E=elk, NONE=none)
File: ElkBehaviorData.csv
Description:
Variables
- Camera: Unique camera deployed at each site.
- Video: The video in which a cervid was identified at each camera location.
- Obs_ID: Unique observation ID combining site (Camera) and observation (Video).
- Bin: Cervid group=Elk
- Behavior1: Behavior exhibited by individual #1 in video.
- Behavior2: Behavior exhibited by individual #2 in video (if >1 individuals)
- Behavior3: Behavior exhibited by individual #3 in video (if >1 individuals)
- Sex1: Sex of individual #1 in video.
- Sex2: Sex of individual #2 in video (if >1 individuals)
- Sex3: Sex of individual #3 in video (if >1 individuals)
- DateTime: Date/time stamp of when an observation occurred.
- Antler1: Antler class of individual #1 in video.
- Antler2: Anlter class of individual #2 in video (if >1 individuals)
- Antler3: Anlter class of individual #3 in video (if >1 individuals)
- Sex4: Sex of individual #4 in video (if >1 individuals)
- Antler4: Anlter class of individual #4 in video (if >1 individuals)
- Behavior4: Behavior exhibited by individual #4 in video (if >1 individuals)
- Duration: Video duration.
- NumTotalElk: The total number of individual elk in each video.
- NumCow: The total number of female elk in each video.
- NumCalfUncertain: The total number of calf or uncertain sex elk in each video.
- NumBull: The total number of male elk in each video.
- Comment: Observer notes.
File: cervid.dat.csv
Description: All cervid data cleaned and pivoted to include behavior, sex, and antler class of each individual (animal) in a give observation. Exported CSV from Data Processing code, and each individual observation manually checked.
Variables
- camera: Unique camera deployed at each site (site ID).
- video: The video in which a cervid was identified at each camera location.
- obs_id: Unique observation ID combining site (camera) and observation (video).
- bin: Cervid genus group (Odocoileous spp = Deer, Cervus canadensis = Elk)
- duration: Video duration in minute:seconds format
- duration_sec: Video duration in seconds (00:00 durations were camera malfunctions that observed behaviors for <1 second; these videos were assigned seconds=1)
- animal: The individual ID for each animal in a given observation (corresponds to behavior, sex, and alter class of individual)
- behavior: Behavior of the individual in a given observation.
- sex: Sex of the individual in a given observation.
- antler: Antler class of the individual in a given observation.
- date_time: Observation timestamp.
- species: Species of the individual in a given observation.
- video_incomplete_corrupt: Flag for incomplete or corrupt videos (i.e., less than 10 seconds we had programmed the camera to record)
- num_total_deer: Total number of deer in the observation (missing for elk).
- num_bucks: Total number of male deer in the observation (missing for elk).
- num_does: Total number of female deer in the observation (missing for elk).
- num_fawns: Total number of deer in the observation (missing for elk).
- comment: Observer notes.
File: edges_direct_final.csv
Description: Edge weights for direct contacts. Cleaned and prepped in Data Cleaning/Process code and manually reformatted to meet network plotting data structure.
Variables
- from: shedding species
- to: uptake species
- weight: edge weight
- liz: site type (reference, water tank, scrape)
- species: shedding species
- selfloop: within species flag (i.e., intraspecific weight)
- competence: under assumption of equal or variable competence
File: edges_indirect_final.csv
Description: Edge weights for indirect contacts. Cleaned and prepped in Data Cleaning/Process code and manually reformatted to meet network plotting data structure.
Variables
- from: shedding species
- to: uptake species
- weight: edge weight
- liz: site type (reference, water tank, scrape)
- species: shedding species
- selfloop: within species flag (i.e., intraspecific weight)
- competence: under assumption of equal or variable competence
File: final.dat.csv
Description: Final cleaned data set used for analyses.
Variables
- camera: Unique camera deployed at each site (site ID).
- set_date: Date camera was deployed.
- lat: Latitude of camera location (decimal degrees)
- long: Longitude of camera location (decimal degrees)
- effort_days: Number of days the camera was operational.
- set_type: Site type: condensed categories of water tank, scrape site, or reference area.
- md_min_male: minutes of male mule deer videos at each site.
- wtd_min_male: minutes of male white-tailed deer videos at each site.
- elk_min_male: minutes of male elk videos at each site.
- md_min_all: minutes of mule deer videos at each site (all sexes/age classes)
- wtd_min_all: minutes of white-tailed deer videos at each site (all sexes/age classes)
- elk_min_all: minutes of elk videos at each site (all sexes/age classes)
- indirect_elk: minutes of indirect (environmental) contact behaviors exhibited by male elk at each site
- tie_elk: seconds of video with tied behaviors for elk (>1)
- direct_elk: minutes of direct contact behaviors exhibited by male elk at each site
- other_elk: minutes of other behaviors exhibited by male elk at each site
- other_mule_deer: minutes of other contact behaviors exhibited by male mule deer at each site
- direct_mule_deer: minutes of direct contact behaviors exhibited by male mule deer at each site
- indirect_mule_deer: minutes of indirect (environmental) contact behaviors exhibited by male mule deer at each site
- tie_mule_deer: seconds of video with tied behaviors for mule deer (>1)
- other_white_tailed: minutes of other contact behaviors exhibited by white-tailed deer at each site
- direct_white_tailed: minutes of direct contact behaviors exhibited by male white-tailed deer at each site
- indirect_white_tailed: minutes of indirect (environmental) contact behaviors exhibited by male white-tailed deer at each site
- tie_white_tailed: seconds of video with tied behaviors for white-tailed deer (>1)
- interaction: Species cooccurence code for each site (M=mule deer, W=white-tailed deer, E=elk, NONE=none)
File: PrevalenceLitReview.csv
Description: All studies returned by Boolean search string: “chronic wasting disease” AND “mule deer” AND “white-tailed deer” AND “elk” AND “prevalence” in Web of Science on March 23rd, 2025.
Variables
- Publication: Type J=Journal Article, S=Book series
- Authors: Article/chapter authors.
- Book Editors: Book editors.
- Article Title: Article/chapter title.
- Source Title: Journal/section name.
- Book Series: Book title.
- Abstract: Used for screening.
- Publication Year: Year the article/book was published.
- Volume: Journal volume.
- Issue: Journal issue.
- Start Page: Article/chapter start page.
- End Page: Article/chapter end page.
- Article Number: for online-only journals with no page numbers.
- DOI: digital object identification number.
- DOI Link: digital object indentification link.
- Book DOI: book digital object identification number.
- Include AllSpecies: If the reference met inclusion criteria and included elk, white-tailed deer, and mule deer in the same study.
- Include Pairwise: If the reference at least two of the following species in the same study: elk, white-tailed deer, and mule deer
- Reason: Exclusion reason.
Code/software
All analyses were conducted in Program R v.4.4.1 (R Core Team, 2024). The provided code is commented to describe the workflow.
Packages used to run the files are as follows:
- library(patchwork)
- library(sf)
- library(mapview)
- library(leaflet)
- library(nnet)
- library(sjPlot)
- library(broom)
- library(janitor)
- library(emmeans)
- library(igraph)
- library(ggraph)
- library(tidygraph)
- library(terra)
- library(ggnewscale)
- library(ggspatial)
- library(tidyverse)
- library(glmmTMB)
- library(ggpubr)
- library(gridExtra)
- library(DHARMa)
- library(broom.mixed)
- library(nnet)
- library(MASS)
- library(tidyverse)
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- NA