DOI: 10.5061/dryad.3cc2702
title: Data from: Direct and indirect effects of pine silviculture on the larval occupancy and breeding of declining amphibian species

description: 1. Plantation silviculture is increasing globally and is particularly
 intensive in temperate coniferous forests, where densely planting trees
 requires practices common to non-conifer systems that can alter forest
 floor microhabitat, and potentially threaten amphibian persistence. Most
 declining amphibian species depend on specific forest microhabitats as
 terrestrial refugia, but amphibian extirpation associated with tree
 harvest alone appears unlikely, suggesting that impacts of planting
 forests on groundcover might better predict recent declines in amphibian
 occupancy. 2. We repeatedly sampled larval presence or absence of 10
 amphibian species native to temperate coniferous forest in the
 Southeastern United States for one year at 62 isolated wetlands located in
 either naturally regenerating or planted forest (plantation) to assess
 three direct ways that planted forests might reduce amphibian breeding
 site occupancy by: 1) increasing conifer densities, 2) decreasing
 groundcover, and 3) an indirect pathway, whereby increased tree densities
 at plantations might reduce groundcover and thus amphibian site occupancy.
 3. After controlling for wetland traits and accounting for differences in
 detection, breeding site occupancy for 8/10 amphibian species was
 dependent upon whether forests were planted surrounding wetlands (within
 300 m). Herbaceous groundcover, not canopy, most commonly influenced
 occupancy and increased occupancy for declining surface active or
 fossorial amphibians. 4. Path analyses showed that, by directly and
 indirectly reducing groundcover (via conifer densities), plantations had
 significantly lower occupancy of two declining surface active or fossorial
 frog species, whereas two common aquatic frog species were tolerant to
 planting conifers. Among declining species, salamanders showed a greater
 reduction in occupancy than anurans, likely because of greater
 vulnerability to the drier forest floor conditions of plantation than
 naturally regenerating forests. 5. Synthesis and applications: Direct
 negative impacts of coniferous plantation on amphibians can be addressed
 by limiting groundcover and soil impacts, including switching from high
 intensity practices, such as mechanical chopping vegetation or bedding
 soil, to lower intensity site preparation treatments that are less likely
 to significantly disturb groundcover. Indirect negative effects of dense
 canopy cover at planted forests could be lowered by periodically thinning
 canopies prior to final harvest, thus increasing intact forest groundcover
 and the conservation of both common and declining amphibians.
description: Analyses R code
 usedAnalyses.RREAD MEMetadata describing variables in all data files.metadata.txtFL_CONDForest Inventory Analysis (FIA) data including estimates of forest habitat structure. See READ ME.txt for variable description.presencehistory_only_sites_w_covariatesDetection histories for 10 amphibian species along with site vegetation measurements. See READ ME.txt for variable definitions.VegetationVisual estimates of vegetation cover taken around wetland study sites. See READ ME.txt for variable definitions.wbfDeclining species site occupancy and site-level vegetation for lavaan modeling. See READ ME.txt for variable definitions.