Geology topics

John J. Cox

Publications and source records attributed to John J. Cox.

7 recordsLinked to original sources

USGS2026

Anuran occupancy of created wetlands within reforested legacy surface mines in Kentucky and West Virginia

Restoration of habitat is an important component of wildlife management. Surface coal mining has altered forest cover in the Central Appalachians, and most reclamation activities on previously mined lands result in non-native grasslands or shrub lands. The Forestry Reclamation Approach (FRA), which emphasizes non-native vegetation removal, soil decompaction, planting of native trees and shrubs, and, in some cases, wetland creation represents an alternative to grassland-based reclamation that may promote forest-associated wildlife on legacy surface mines. We used automated recording units to evaluate the response of anurans to created wetlands and the FRA in Kentucky and West Virginia, USA. We used a Bayesian community occupancy model to compare species occupancy and richness across a range of wetland sizes (6.6–252 m 2 ) and 3 site types: 1) younger FRA (1–6 yr), 2) older FRA (7–23 yr), and 3) unmined, mature forests (>100 yr). In addition, we evaluated factors influencing anuran detection probabilities. Mean occupancy and species richness in both states were highest in the younger FRA, suggesting anurans may rapidly colonize wetlands created on restored mines. In Kentucky, occupancy of several species (green frog [ Lithobates clamitans ], pickerel frog [ L. palustris ], and wood frog [ L. sylvaticus ]) was higher in larger created wetlands, but wetland size was not important in West Virginia. Daily minimum temperature positively influenced detection of anurans in both states, and time of day was also important for detection in West Virginia. Wetland creation and implementation of the FRA may be an important tool for wildlife managers aiming to improve anuran populations and diversity on legacy surface mines in the Central Appalachians.

Kentucky, West Virginia↗

USGS2025

Initial responses of songbird communities to forest reclamation on legacy surface mines

Surface coal mining and subsequent reclamation efforts in the Appalachian Mountains, USA, transform the ecological characteristics of natural landscapes. The Forestry Reclamation Approach (FRA) is a mine reclamation method that emphasizes best management practices in forestry. FRA practices have demonstrated success in establishing native forests and accelerating natural succession on coal mines; however, no studies have empirically examined the effects of the FRA on bird communities. Our study aimed to assess the avian community composition within young forests reclaimed using the FRA after one decade of forest growth. Whereas traditional reclamation practices often support grassland avian guilds, we expected that the FRA would provide habitat for shrubland and young forest avian guilds. Moreover, we sought to determine whether FRA forests would contain known avian indicator species of the native forest land cover. In June 2022, we conducted point count surveys in high-elevation, red spruce-northern hardwood (RS-NH) forests in the Appalachian Mountains of eastern West Virginia, USA. Using Bayesian multispecies occupancy models, we assessed avian guild occupancy and species richness within two FRA forest age classes (2–5 years and 8–11 years). We also examined avian community composition within two older RS-NH reference age classes to predict the future avian composition within FRA forests if reclamation succeeds. We found that the FRA breeding bird community included all of the avian indicator species expected to inhabit a young RS-NH forest. These results suggest that after approximately one decade, legacy mines reclaimed using the FRA are progressing toward a native RS-NH forest that supports associated forest bird communities.

West Virginia↗

USGS2024

Wetland creation and reforestation of legacy surface mines in the Central Appalachian Region (USA): A potential climate-adaptation approach for pond-breeding amphibians?

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 8–11-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.

West Virginia↗

USGS2020

Terrestrial wildlife in the post-mined Appalachian landscape: Status and opportunities

Coal mining is an anthropogenic stressor that has impacted terrestrial and semi-aquatic wildlife in the Appalachian Plateau since European settlement. Creation of grassland and early-successional habitats resulting from mining in a forested landscape has resulted in novel, non-analog habitat conditions. Depending on the taxa, the extent of mining on the landscape, and reclamation practices, effects have ranged across a gradient of negative to positive. Forest-obligate species such as woodland salamanders and forest-interior birds or those that depend on aquatic systems in their life cycle have been most impacted. Others, such as grassland and early-successional bird species have responded favorably. Some bat species, as an unintended consequence, use legacy deep mines as winter hibernacula in a region with limited karst geology. Recolonization of impacted wildlife often depends on life strategies and species’ vagility, but also on altered or arrested successional processes on the post-surface mine landscape. Many wildlife species will benefit from Forest Reclamation Approach practices going forward. In the future, managers will be faced with decisions about reforestation versus maintaining open habitats depending on the conservation need of species. Lastly, the post-mined landscape currently is the focal point for a regional effort to restore elk ( Cervus canadensis ) in the Appalachians.

Appalachian Plateau↗

USGS2019

Spatial capture–recapture for categorically marked populations with an application to genetic capture–recapture

Recently introduced unmarked spatial capture–recapture (SCR), spatial mark–resight (SMR), and 2‐flank spatial partial identity models (SPIMs) extend the domain of SCR to populations or observation systems that do not always allow for individual identity to be determined with certainty. For example, some species do not have natural marks that can reliably produce individual identities from photographs, and some methods of observation produce partial identity samples as is the case with remote cameras that sometimes produce single‐flank photographs. Unmarked SCR, SMR, and SPIM share the feature that they probabilistically resolve the uncertainty in individual identity using the spatial location where samples were collected. Spatial location is informative of individual identity in spatially structured populations because a sample is more likely to have been produced by an individual living near the trap where it was recorded than an individual living further away from the trap. Further, the level of information about individual identity that a spatial location contains is related to two key ecological concepts, population density and home range size, which we quantify using a proposed Identity Diversity Index (IDI). We show that latent and partial identity SCR models produce imprecise and biased density estimates in many high IDI scenarios when data are sparse. We then extend the unmarked SCR model to incorporate categorical, partially identifying covariates, which reduce the level of uncertainty in individual identity, increasing the reliability and precision of density estimates, and allowing reliable density estimation in scenarios with higher IDI values and with more sparse data. We illustrate the performance of this “categorical SPIM” via simulations and by applying it to a black bear data set using microsatellite loci as categorical covariates, where we reproduce the full data set estimates with only slightly less precision using fewer loci than necessary for confident individual identification. We then discuss how the categorical SPIM can be applied to other wildlife sampling scenarios such as remote camera surveys, where natural or researcher‐applied partial marks can be observed in photographs. Finally, we discuss how the categorical SPIM can be added to SMR, 2‐flank SPIM, or other latent identity SCR models.

Ecosphere↗

USGS2019

Early genetic outcomes of American black bear reintroductions in the Central Appalachians, USA

Habitat loss and overexploitation extirpated American black bears (Ursus americanus) from most of the Central Appalachians, USA, by the early twentieth century. To attempt to restore bears to the southwestern portion of this region, 2 reintroductions that used small founder groups (n = 27 and 55 bears), but different release methods (hard versus soft), were conducted during the 1990s. We collected hair samples from black bears in the reintroduced Big South Fork (BSF) and Kentucky–Virginia populations (KVP), their respective Great Smoky Mountains (GSM) and Shenandoah National Park (SNP) source populations, and a neighboring population in southern West Virginia (SWV) to investigate the early genetic outcomes of bear reintroduction. Despite having undergone genetic bottlenecks, genetic diversity remained similar between reintroduced populations and their sources ~15 years after the founder events (ranges: AR = 4.86–5.61; HO = 0.67–0.75; HE = 0.65–0.71). Effective population sizes of the reintroduced KVP and BSF (NE = 31 and 36, respectively) were substantially smaller than their respective SNP and GSM sources (NE = 119 and 156, respectively), supporting founder effects. Genetic structure analysis indicated that the hard released (i.e., no acclimation period) KVP founder group likely declined considerably, whereas the soft released BSF founder group remained mostly intact, suggesting superior effectiveness of soft releases. Asymmetrical gene flow via immigration from the SWV has resulted in the KVP recovering from the initial founder group reduction. Sustained isolation, small NE, and small population size of the BSF may warrant continued genetic monitoring to determine if gene flow from neighboring populations is established or NE declines. For future bear reintroductions, we suggest managers consider sourcing founders from populations with high genetic diversity and soft-releasing bears to locales that are, if possible, within the dispersal capability of extant populations to mitigate the potential consequences of founder effects and isolation.

Central Appalachians↗

USGS2015

Rapid growth and genetic diversity retention in an isolated reintroduced black bear population in the central appalachians

Animal reintroductions are important tools of wildlife management to restore species to their historical range, and they can also create unique opportunities to study population dynamics and genetics from founder events. We used non-invasive hair sampling in a systematic, closed-population capture-mark-recapture (CMR) study design at the Big South Fork (BSF) area in Kentucky during 2010 and Tennessee during 2012 to estimate the demographic and genetic characteristics of the black bear ( Ursus americanus ) population that resulted from a reintroduced founding population of 18 bears in 1998. We estimated 38 (95% CI: 31–66) and 190 (95% CI: 170–219) bears on the Kentucky and Tennessee study areas, respectively. Based on the Tennessee abundance estimate alone, the mean annual growth rate was 18.3% (95% CI: 17.4–19.5%) from 1998 to 2012. We also compared the genetic characteristics of bears sampled during 2010–2012 to bears in the population during 2000–2002, 2–4 years following reintroduction, and to the source population. We found that the level of genetic diversity since reintroduction as indicated by expected heterozygosity ( H E ) remained relatively constant ( H E(source, 2004)  = 0.763, H E(BSF, 2000–2002)  = 0.729, H E(BSF, 2010–2012)  = 0.712) and the effective number of breeders ( N B ) remained low but had increased since reintroduction in the absence of sufficient immigration ( N B(BSF, 2000–2002)  = 12, N B(BSF, 2010–2012)   = 35). This bear population appears to be genetically isolated, but contrary to our expectations, we did not find evidence of genetic diversity loss or other deleterious genetic effects typically observed from small founder groups. We attribute that to high initial genetic diversity in the founder group combined with overlapping generations and rapid population growth. Although the population remains relatively small, the reintroduction using a small founder group appears to be demographically and genetically sustainable.

Kentucky, Tennessee↗