Data from: Environmental detection of the amphibian chytrid fungus in water bodies is associated with host infection along a deforestation gradient

Data files

Jun 24, 2026 version files 151.22 KB

Applied_Ecol_Code_Analysis.Rmd

46.22 KB
Bd_env_host_corr_dataset.csv

2.31 KB
Bd_env_host_dataset.csv

90 KB
README.md

12.68 KB

Abstract

This data package contains environmental and host-associated data used to investigate the distribution of the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), across eight Atlantic Forest landscapes in southeastern Brazil. The repository includes (1) a primary dataset for environmental, host, and landscape-level variables, (2) a site-level dataset for the relationship between environmental Bd concentration and host infection load, (3) an R Markdown script to reproduce the statistical analyses and figures presented in the associated publication, and (4) a README file describing the repository contents.

The main dataset includes geographic information, landscape identifiers, forest-type classification, amphibian species identity, water-sampling information, Bd detection and quantification data obtained by digital and real-time quantitative PCR detection assays, Bd lineage information, and environmental and landscape metrics used in statistical analyses.

The data can be used to investigate relationships among environmental pathogen occurrence, host infection patterns, habitat structure, and landscape integrity, and to support related studies that use these variables.

https://doi.org/10.5061/dryad.1g1jwsvd1

Related manuscript submitted to Journal of Applied Ecology

Files Included

See further down for list of variables.

1. Bd_env_host_dataset.csv

Main dataset used in the study.

This file contains environmental and host-associated data collected from eight Atlantic Forest landscapes in southeastern Brazil.

Data include:

Site and landscape identifiers
Geographic coordinates
Forest type (continuous or fragmented)
Amphibian species identity
Water sampling information
Environmental and host-associated Batrachochytrium dendrobatidis (Bd) detection, concentration, and infection load data obtained using dPCR and qPCR
Bd genotype information
Landscape metrics and environmental variables used in statistical analyses

Each row corresponds to a single environmental sample or amphibian sample.

2. Bd_env_host_corr_dataset.csv

Dataset used to evaluate the relationship between Bd loads in amphibian hosts and Bd concentration in water samples.

This file contains site-level summaries of:

Mean host Bd infection load by site
Environmental Bd concentration in water samples by site
Forest type
Landscape identity

These data were used in the correlation analyses reported in the manuscript.

3. Applied_Ecol_Code_Analysis.Rmd

R Markdown script used to reproduce the statistical analyses and figures presented in the manuscript.

Analyses include:

Correlation analyses
Non-parametric tests
Generalized linear mixed models
Figure generation

Software

R version: 4.4.0

Main packages:

ggplot2
dplyr
glmmTMB
DHARMa
performance
visreg
MASS
car
MuMIn
binom

Data Notes

Bd = Batrachochytrium dendrobatidis

All analyses can be reproduced using the provided R Markdown file and datasets.

File format

All tabular data files are provided in CSV format.

Delimiter: comma (,)
Decimal notation: period (.)
Missing values are coded as NA throughout all datasets.No blank cells are intentionally used.

Variable Definitions

Variable abbreviation	Definition
sample_id	Unique identifier assigned to each sample included in the dataset
local_id	Identifier of the site where the sample was collected
landscape	Landscape identifier corresponding to one of the eight study landscapes
longitude_deg	Geographic longitude of the sampling location in decimal degrees
latitude_deg	Geographic latitude of the sampling location in decimal degrees
forest_type	Forest cover category of the landscape (Continuous / Fragmented)
source	Sample source type (Water / Host)
elevation	Elevation of the sampling location above sea level (m)
date	Date on which the sample was collected
frog_species	Scientific name of the amphibian species sampled
water_vol	Volume of water filtered for environmental DNA analysis (L)
bd_water_dPCR_cpL	Concentration of Batrachochytrium dendrobatidis (Bd) DNA in water estimated by digital PCR (dPCR), expressed as DNA copies per liter of filtered water (copies/L)
bd_water_detec_dpcr	Bd detection status in water determined by dPCR (0 = not detected; 1 = detected)
bd_water_dPCR_LOG10	Base-10 logarithm of Bd DNA concentration in water estimated by dPCR
bd_water_qPCR_cpL	Concentration of Bd DNA in water estimated by quantitative PCR (qPCR), expressed as DNA copies per liter of filtered water (copies/L)
bd_water_qPCR_LOG10	Base-10 logarithm of Bd DNA concentration in water estimated by qPCR
bd_qPCR_host	Bd infection load measured from amphibian skin swabs using qPCR, expressed as DNA copies per swab (copies/swab)
bd_host_qPCR_LOG10	Base-10 logarithm of host Bd infection load measured by qPCR
bd_detection_qpcr	Bd detection status in host skin swabs determined by qPCR (0 = not detected; 1 = detected)
bd_host_genotype	Bd genotype identified from the host sample
% Floresta_250	Percentage of forest cover; 250 m radius
den_dre_local	Drainage density; 250 m radius (m ha⁻¹)
percen_dre_local	Drainage percentage; 250 m radius
n_dre	Number of drainages; 250 m radius
den_bor_local	Forest edge density; 250 m radius (total length (m) of the edges in the landscape)
den_app_local	Edge density by riparian protected area; 250 m radius (total length (m) of the edges only in riparian protected forests in the landscape)
den_frag_local	Edge density by forest fragment; 250 m radius (total length (m) of the edges of fragmented forests in the landscape)
TamFrag_m2	Fragment size (area, m²)
habitat_split_pon	Habitat split - ponds: Spatial discontinuity between natural forest vegetation and ponds
habitat_split_stream	Habitat split - streams: Spatial discontinuity between natural forest vegetation and streams
cob_veg_land	Percentage of forest cover; 10-km radius
app_land	Percentage of riparian protected areas; 10-km radius
frags_land	Percentage of forest only comprising fragmented areas; 10-km radius
den_bor_land	Forest edge density; 10-km radius (total length (m) of the edges in the landscape)
den_frag_land	Edge density by forest fragment; 10-km radius (total length (m) of the edges of fragmented forests in the landscape)
den_app_land	Edge density by riparian protected area; 10-km radius (total length (m) of the edges only in riparian protected forests in the landscape)
n_frag_land	Number of forest fragments within the landscape; 10-km radius
den_dre_land	Drainage density in the landscape; 10-km radius (m ha⁻¹)
dre_land	Drainage percentage; 10-km radius
m_agua_land	Water mass percentage; 10-km radius
dren_app_land	Drainage percentage within riparian protected areas; 10-km radius
den_dre_app_land	Drainage density in riparian areas; 10-km radius (m ha⁻¹)
ennd_frag_land	Euclidean nearest-neighbor distance – fragments: Average distance (m) between all forest fragments within the landscape
ennd_app_land	Euclidean nearest-neighbor distance – riparian protected areas: Average distance (m) between all riparian protected forests within the landscape
bd_qPCR_mean_host	Mean Batrachochytrium dendrobatidis (Bd) infection load measured from amphibian skin swabs using qPCR (copies/swab)
bd_qPCR_SD_host	Standard deviation of Bd infection load measured from amphibian skin swabs using qPCR (copies/swab)
bd_qPCR_LOG10_mean_host	Base-10 logarithm of the Bd mean infection load measured from amphibian skin swabs using qPCR (log10 copies/swab)
bd_qPCR_water	Bd DNA quantity in water estimated by qPCR (total number of copies)
bd_qPCR_LOG10_water	Base-10 logarithm of Bd DNA quantity in water estimated by qPCR (log10 copies)
bd_qPCR_water_cpL	Bd DNA concentration in water estimated by qPCR (copies/L)
bd_qPCR_water_log_cpL	Base-10 logarithm of Bd DNA concentration in water (log10 copies/L)