Wetland creation and reforestation of legacy surface mines in the Central Applachian Region (USA): A potential climate-adaptation approach for pond-breeding amphibians?
Data files
Apr 24, 2024 version files 35.45 KB
Abstract
Habitat restoration and creation within human-altered landscapes can buffer the impacts of climate change on wildlife. The Forestry Reclamation Approach (FRA) is a coal surface mine reclamation practice that enhances reforestation through soil decompaction and the planting of native trees. Recently, wetland creation has been coupled with FRA to increase habitat available for wildlife, including amphibians. Our objective was to evaluate the response of pond-breeding amphibians to the FRA by comparing species occupancy, richness, and abundance across two FRA age-classes (2–5-year and 8–1—year reclaimed forests), traditionally reclaimed sites that were left to naturally regenerate after mining, and in mature, unmined forests in the Monongahela National Forest (West Virginia, USA). We found that species richness and occupancy estimates did not differ across treatment types. Spotted Salamanders (Ambystoma maculatum) and Eastern Newts (Notophthalmus viridescens) had the greatest estimated abundances in wetlands in the older FRA treatment. Additionally, larger wetlands had greater abundances of Eastern Newts, Wood Frogs (Lithobates sylvaticus), and Green Frogs (L. clamitans) compared to smaller wetlands. Our results suggest that wetland creation and reforestation increases the number of breeding sites and promotes microhabitat and microclimate conditions that likely maximize the resilience of pond-breeding amphibians to anticipated climate changes in the study area.
README: Wetland creation and reforestation of legacy surface mines in the Central Applachian Region (USA): A potential climate-adaptation approach for pond-breeding amphibians?
https://doi.org/10.5061/dryad.866t1g1zf
Description of the data and file structure
R script and data used to estimate species’ occupancy, species richness, and abundance of pond-breeding amphibians in wetlands on reforested surface mines in the Monongahela National Forest, WV, USA.
File list (files found within Sherman_et_al_2024.zip)
Multi-species Occupancy Model
Sherman_et_al_2024_multispecies_occupancy.R
aame.csv
amac.csv
hscu.csv
hver.csv
lcla.csv
lpal.csv
lsyl.csv
nvir.csv
pcru.csv
SiteCovariates.csv
SurveyCovariates.csv
Abundance Model
Sherman_et_al_2024_abundance.R
Sherman_et_al_2024_countdata.csv
File Descriptions
Multi-species Occupancy Model
Sherman_et_al_2024_multispecies_occupancy.R – The file loads amphibian encounter matrices (i.e., aame.csv), formats data for WinBUGS model, and summarizes posterior distributions.
aame.csv - encounter matrix for Anaxyrus americanus
amac.csv - encounter matrix for Ambystoma maculatum
hscu.csv - encounter matrix for Hemidactylium scutatum
hver.csv - encounter matrix for Hyla versicolor
lcla.csv - encounter matrix for Lithobates clamitans
lpal.csv - encounter matrix for Lithobates palustris
lsyl.csv - encounter matrix for Lithobates sylvaticus
nvir.csv - encounter matrix for Notophthalmus viridescens
pcru.csv - encounter matrix for Pseudacris crucifer
SiteCovariates.csv – site covariates used in the multi-species occupancy model
Descriptions of variables
YFRA – Younger (2-5 yrs) Forestry Reclamation Approach treatment
OFRA – Older (8-11 yrs) Forestry Reclamation Approach treatment
REGEN - Traditionally reclaimed treatment
MAT – mature, unmined forest treatment
zArea – Standardized area (m2) of wetlands sampled
Area = Unstandardized area (m2) of wetlands sampled
zCC – Standardized canopy cover
CC – canopy cover
pH – pH (H+)
TOC - Total Organic Carbon (TOC (mg/L)
Al - Al (mg/L)
Mn- Mn (mg/L)
Cond - conductivity (μS cm−1)
Turb - turbidity (FTU)
Cl - Cl (mg/L)
SO4 - SO4 (mg/L)
NO3-N - NO3-N (mg/L)
NH4-N - NH4-N (mg/L)
Ca - Ca+2 (mg/L)
Mg - Mg+2 (mg/L)
K - K+ (mg/L)
Na - Na+ (mg/L)
Fe - Fe (mg/L)
NO2-N - NO2-N (mg/L)
SurveyCovariates.csv – sampling covariates used in the multi-species occupancy model
Descriptions of variables
YFRA – Younger (2-5 yrs) Forestry Reclamation Approach treatment
OFRA – Older (8-11 yrs) Forestry Reclamation Approach treatment
REGEN - Traditionally reclaimed treatment
MAT – mature, unmined forest treatment
zD1 – standardized day of year for first sampling event
zD2 – standardized day of year for second sampling event
zD3 – standardized day of year for third sampling event
zD4 - standardized day of year for fourth sampling event
Abundance Model
Sherman_et_al_2024_abundance.R – The file loads amphibian count data, site and sampling covariates, formats data for WinBUGS, and summarizes posterior distributions.
Sherman_et_al_2024_countdata.csv – includes count data for all species and site and sampling covariates
Descriptions of variables
YFRA – Younger (2-5 yrs) Forestry Reclamation Approach treatment
OFRA – Older (8-11 yrs) Forestry Reclamation Approach treatment
REGEN - Traditionally reclaimed treatment
MAT – mature, unmined forest treatment
zAream2 - Standardized area (m2) of wetlands sampled
Date1, Date2, Date3, Date 4 – Day of Year when sampling occurred
Amphibian count data – for example AMAC.1 = count data for Ambystoma maculatum during sampling event 1. See encounter matrix in multi-species occupancy model for species scientific names
Note: All of the files in DataS1 must be within your working directory for the analysis to work. Users will also have to download WinBUGS.