Risk factors and coinfection dynamics of pathogens in wild turkeys (Meleagris gallopavo) from Pennsylvania, USA
Data files
Mar 09, 2026 version files 266.03 KB
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Code_new.R
36.76 KB
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Cooccur_analysis_new.csv
6.87 KB
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LPDVdataNEW1.csv
217.34 KB
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README.md
5.06 KB
Abstract
Interactions between co-occurring pathogens can have complex and significant impacts on host survival, fitness, and population dynamics. While common in wildlife, coinfections are often overlooked, and research may create biased management perspectives when individual pathogens are assessed in isolation. Recent work has found that wild turkeys (Meleagris gallopavo) are affected by various pathogens, but it is unknown how infections and coinfections are spatially structured or interact with each other. Here, we determined the associations and risk factors of infection by lymphoproliferative disease virus (LPDV), reticuloendotheliosis virus (REV), three avian Mycoplasma species, and internal parasites in Pennsylvania wild turkeys. Our results indicate varying prevalences: LPDV (70%), REV (1%), Mycoplasma gallisepticum (0%), Mycoplasma meleagridis (4%), Mycoplasma synoviae (2%), and internal parasites (63%). The prevalence of LPDV was greater in adults than juveniles but did not vary with year, sex, study area, or landscape type. Parasite species richness was greater in juveniles than adults, greater in males than females, varied by year and study area, but did not vary with landscape type. Coinfections with LPDV and parasites were more common (41%) than infections with only LPDV (26%) or only parasites (22%). All other coinfection prevalences involving viruses, Mycoplasma species, and parasites were low (0–3%). Finally, infection with LPDV did not differ with overall parasite species richness but was negatively associated with infection with parasitic nematodes. These results reveal high rates of coinfections with LPDV and parasites in turkeys but suggest that parasite infections are independent of LPDV infections. Ongoing work is currently investigating the sublethal effects of these coinfections on wild turkey populations.
Files description:
- Code_new.R - Main code file.
- LPDVdataNEW1.csv - Data file used to run all models and figures. Contains metadata linked to individual turkeys.
- Cooccur_analysis_new.csv - Data file formatted specifically to run cooccurrence analysis and generate a figure.
Variable and column description:
Variables within "LPDVdataNEW1.csv"
- bandid - unique individual turkey ID linked to all metadata.
Linked to columns below from 'MG' to 'long'.
- MG - infection with Mycoplasma gallisepticum (1 = infected, 0 = not infected)
- MS - infection with Mycoplasma synoviae (1 = infected, 0 = not infected)
- MM - infection with Mycoplasma meleagridis (1 = infected, 0 = not infected)
- Capillaria - infection with Capillaria (1 = infected, 0 = not infected)
- Eimeria - infection with Eimeria (1 = infected, 0 = not infected)
- Ascarids - infection with Ascarids (1 = infected, 0 = not infected)
- Syngamus - infection with Syngamus (1 = infected, 0 = not infected)
- Tetrameres - infection with Tetrameres (1 = infected, 0 = not infected)
- Isospora - infection with Isospora (1 = infected, 0 = not infected)
- Raillietina - infection with Raillietina (1 = infected, 0 = not infected)
- Choanotaenia - infection with Choanotaenia (1 = infected, 0 = not infected)
- Strongylid - infection with Strongylid (1 = infected, 0 = not infected)
- coinfection - simultaneous infection with any given parasite species and LPDV (1 = coinfected, 0 = not coinfected)
- Parasites - infection with a number of parasites (0 to 4)
- LPDV_cat - infection with LPDV (Pos = infected, Neg = not infected)
- LPDV - infection with LPDV (1 = infected, 0 = not infected)
- REV - infection with REV (1 = infected, 0 = not infected)
- age - age, juvenile or adult (J, A)
- sex - sex, female or male (F, M)
- captyr - year (2022, 2023, 2024, 2025)
- studyarea - study area, Wildlife Management Unit (2D, 3D, 4D, 5C)
- sitechar - landscape type; agricultural (AG), forested opening (FO), other (O)
- lat - latitude coordinate where each turkey was captured
- long - longitude coordinate where each turkey was captured
- virus - mutually exclusive infection categories for either LPDV or REV.
Linked to the 'infection' column below.
- infection - infection data for either LPDV or REV (1 = infected, 0 = not infected)
- lon_site - unique longitude coordinate for each collecting site.
- Linked to columns below from 'lat_site' to 'Group_size'.
- lat_site - unique latitude coordinate for each collecting site
- LPDV_prev - LPDV prevalence for each collecting site
- group_number - unique group number ID for each collecting site
- Group_size - number of turkeys collected for each collecting site
- Type - type of each parasite species found in this study. Linked to
- columns below from 'Position' to 'Percent'.
- Position - a position number to help format the parasite prevalence figure
- Parasite_sp. - each parasite species found in this study
- Infected - number of turkeys infected with a specific species of parasite
- Total - total number of turkey samples examined for parasites
- Prevalence - prevalence of each parasite species found in this study, expressed as a proportion
- Percent - prevalence of each parasite species found in this study, expressed as a percent
- WMU - wildlife management units.
Linked to columns below from 'Parasite_sp._wmu' to 'Prevalence_wmu'.
- Parasite_sp._wmu - names of the top 3 most prevalent parasite species for each WMU
- Prevalence_wmu - prevalence of the top 3 most prevalent parasite species for each WMU
- Parasite_Prev_county - Parasite prevalence for each county.
Linked to columns below from 'LPDV_Prev_county' to 'County'.
- LPDV_Prev_county - LPDV prevalence for each county
- County - name of Pennsylvania county
NA - data not available for a specific cell in the file
Variables within "Cooccur_analysis_new.csv"
- species - unique ID for individual turkeys
- LPDV - infection with LPDV (1 = infected, 0 = not infected)
- Capillaria sp. - infection with Capillaria (1 = infected, 0 = not infected)
- Eimeria sp. - infection with Eimeria (1 = infected, 0 = not infected)
- Ascarids - infection with Ascarids (1 = infected, 0 = not infected)
Software needed:
All analyses were conducted in R version 4.4.1 with RStudio
Packages used:
library(car) # for various stats, like Anova, VIF, etc. (version 3.1-3)
library(cooccur) # for cooccurrence analysis and figure (version 1.3)
library(DHARMa) # for glmm residuals (version 0.4.7)
library(emmeans) # for posthoc (version 1.10.5)
library(lme4) # for glmms (version 1.1-35.5)
library(ggplot2) # for figures (version 4.0.2)
library(wesanderson) # for color palette (version 0.3.7)
library(sf) # for maps (version 1.0-18)
library(maps) # for maps (version 3.4.2.1)
library(dplyr) # for piechart figure (version 1.1.4)
library(gridExtra) # for combining figures (version 2.3)