DOI: 10.5061/dryad.866t1g1zf
title: Wetland creation and reforestation of legacy surface mines in the Central Applachian Region (USA): A potential climate-adaptation approach for pond-breeding amphibians?

description: 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.
description: # 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](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.