The use of Light Detection and Ranging (LiDAR) information is gaining popularity, however its use has been limited in deciduous forests. This thesis describes two studies using LiDAR data in an Eastern Kentucky deciduous forest. The first study quantifies vertical error of LiDAR derived digital elevation models (DEMs) which describe the forests terrain. The study uses a new method which eliminates Global Positioning System (GPS) error. The study found that slope and slope variability both significantly affect DEM error and should be taken in to account when using LiDAR derived DEMs. The second study uses LiDAR derived forest vegetation and terrain metrics to predict terrestrial Plethodontid salamander abundance across the forest. This study used night time visual encounter surveys coupled with zero-inflation modeling to predict salamander abundance based on environmental covariates. We focused on two salamander species, Plethodon glutinosus and Plethodon kentucki. Our methods produced two different best fit models for the two species. Plethodon glutinosus included vegetation height standard deviation and water flow accumulation covariates, while Plethodon kentucki included only canopy cover as a covariate. These methods are applicable to many different species and can be very useful for focusing management efforts and understanding species distributions across the landscape.

Despite being one of the most recognizable sea creatures in the world, sharks remain widely misunderstood by the public. Media coverage often sensationalizes them as dangerous creatures, when in reality, humans pose a much more significant threat to sharks than vice versa. Over the past few decades, overfishing has decimated populations worldwide as demand increases for byproducts such as meat, cartilage, and fins in particular, a crucial ingredient in the Chinese delicacy of shark fin soup. Finning, a particularly inefficient practice that promotes overfishing and waste, occurs when fishers cut off fins at sea and throw carcasses overboard. As sharks play an important role in marine ecosystems as apex predators and are slow to reproduce, increased attention to shark conservation is urgently needed. Although there have been attempts by international organizations such as the United Nations and by individual countries, current legislation has proven to be inadequate in combating shark exploitation. Though public awareness is on the rise thanks to increased media coverage and environmental advocacy, sharks still need greater protection in the face of overharvest and stock depletion. This thesis details the current state of shark exploitation, including shark biology, public perceptions of sharks, and current levels of shark finning, as well as the economics behind the trade. It also analyzes previous actions taken both at the international and national levels. Finally, it recommends further actions to be undertaken in order to preserve declining shark populations and keep them from extinction.

In karst areas relationships between activities occurring on the surface and the overall health of the subsurface environment are often highly interconnected. However, the complex nature of karst flow systems can often make identification of these connections difficult. Carroll Cave, a large stream cave system located in the central Missouri Ozarks, is known for its biological and speleological significance. A dye tracing project to delineate a Carroll Cave recharge area through dye tracing has identified an area of 18.5 km2 which contributes water to the cave. The water from Thunder River within Carroll Cave was positively traced to eight springs of the thirteen springs at a distributary spring system known as Toronto Springs. Through examination of the geochemistry of the individual springs, differences in water chemistry between the various outlets has become evident. Additional work with YSI Sonde dataloggers and consideration of carbonate chemistry relationships has sought to further define the variations in hydrochemical behavior, thus aiding in the discrimination potential spring sources. Primary sources thought to contribute water to the spring system include Carroll Cave and Wet Glaize Creek, with some minor influence from other losing streams in the vicinity. Seepage runs along Wet Glaize Creek have also identified major losing reaches, in close proximity to structural features, which may contribute water to Toronto Springs. Examination of the measured parameters and derived have identified that Carroll Cave and Wet Glaize Creek are the primary end members for Ca2+, Mg2+, HCO3-, specific conductance, and temperature. Using these parameters a two end member mixing model has been developed which describes the mixing zone setting at Toronto Springs and calculates the average proportions of flow contributions by the end members. By using a multi-proxy approach of dye tracing, seepage runs, and geochemistry for the individual springs, the source waters and pathways for the springs at Toronto Springs have been identified.

Surface coal mining is a major form of land change and environmental degradation in Central Appalachia. Traditional mine reclamation iresults in unmanaged, unproductive grasslands that fail to mitigate many of the environmental costs of coal mining and are of minimal use to communities. Forestry reclamation is an alternative reclamation tactic that has the potential to address both environmental and socioeconomic concerns in Central Appalachia. A case study of Laurel Fork Mine in Eastern Kentucky is included.

After sixty-two years of U.S. military testing, the small Puerto Rican island of Vieques and its residents continue to fight against ongoing environmental and social effects of U.S. hegemony. Starting with the arrival of the Spanish, then with U.S. occupation and use of Vieques as a military stopover, Viequense residents are used to U.S. governmental presence on their land. Despite the military’s removal from Vieques in 2003, many local residents have a fundamental lack of trust for the U.S. government. Because of this lack of trust and transparency with U.S. governmental actions in the post- World War II period, residents of Vieques do not see any difference between the USFWS, the EPA, CH2M Hill, and the U.S. Navy. However, many acknowledge that the U.S. government’s involvement may be good for the island, so there is some ambivalence about the U.S. government’s continued presence on the island, its role in developing Vieques, and bettering its current economic situation. While the majority of local activists claim that naval activities negatively affected island life through contamination of land and surrounding waters, also resulting in a range of human health problems, others argue that the U.S. Navy should not be demonized, and the island’s role in conservation should be paramount. These differing views reflect two opposing frameworks: one fighting against a colonizer and U.S. hegemony, and the other promoting a primarily conservation-based framework meant to protect non-human residents.

Over the last few decades coral reefs have faced unprecedented declines in health due to natural and anthropogenic sources. Until recently few studies have examined genotypic variation of growth and thermal stress resistance in Acropora cervicornis. This study aims to assess the potential for energy trade-offs between growth and thermal stress resistance by following 120 coral fragments from 12 genotypes of Acropora cervicornis over the course of 15 months to determine average growth rates for each genotype. Following the completion of the growth observation a bleaching event occurred in the lower Florida Keys providing the opportunity for examining thermal stress resistance. We found that the coral genotype had a significant effect on growth and survival; however no significant correlation was observed between growth under normal conditions and thermal stress resistance. This result shows that there is not a trade-off between growth and thermal stress resistance and that a genotype’s ability to resist thermal stress cannot be predicted from growth under normal conditions. The lack of a trade-off facilitates intraspecific competition. For genotypes with similar thermal stress tolerances but different growth characteristics, the increase in frequency of disturbances could result in the increased abundance of faster growing genotypes relative to the slow growing genotypes. These results emphasize the importance of maintaining coral nurseries as gene banks to protect the genetic diversity of the reef area in which it is located. Through protecting a wide variety of genotypes, the likelihood of preserving those that have a high thermal tolerance, disease resistance, or faster growth rates is increased.

Seagrass meadows offshore Ras Ghanada, as elsewhere, are an important component to the ecosystem providing numerous benefits to both aquatic and human life. This work focused on mapping the spatial and temporal distribution of seagrass meadows offshore Ras Ghanada using aerial photography acquired in 1996 and high-resolution satellite images captured in 2006 and 2012. The movements of sand shoals were also tracked, so as to further explain the dynamics of this ecosystem, as it is the area between the shoal crests that hosts the best developed seagrass meadows. The natural limiting factor for seagrass on the Ras Ghanada coastal shelf seems to be the fact that they cannot inhabit the (mobile) crests of the sand shoals, but rather, are restricted to the (more stable) sands of the shoal troughs. In the considered time period, both sand shoals and seagrass meadows migrated predominantly in a southeastern direction. The changes of seagrass that occurred in this study occurred on a fairly rapid timescale, in such that they were able to come back when there was disturbance as long as they had available habitat to move into. Furthermore, although seagrass cover declined by 3.4% from 1996 – 2012, there was a greater increase than decline in the areal coverage of seagrass post-Khalifa port construction in 2010. If sediments offshore Ras Ghanada can remain stable and the waters are not polluted by further construction, seagrasses should continue to thrive in the future.

The Veracruz Reef System (VRS) is located in the southwestern Gulf of Mexico. It is comprised of 28 coral reefs in various stages of development and conservation. They are protected under the Parque Nacional Sistema Arrecifal Veracruzano National Park created in 1992. There are many threats to the reefs of the VRS, including the Port and city of Veracruz, which hosts half a million inhabitants and Mexico’s oldest active port. The inhabitants of Veracruz have used reef resources for thousands of years, as evidenced in archaeological sites on Sacrificios island, and constructions throughout the city, most notably in the San Juan de Ulúa Fort which was built entirely of coral skeletons. Despite the usage and protection given under the National Park, there is relatively little known about the health and condition of the stony corals in the System. There has only been one large scale study of 21 reefs conducted in the VRS in the late 1980’s. Since then, the National Park was created and 28 reefs are now recognized. This study performed point-intercept transects on 24 of these reefs including five reefs added to the official list in 2012. Point-intercept transects were surveyed at 63 sites between 2007 and 2014. Percent cover was calculated for seven functional groups. Additionally, demographic data of a subset of individual stony coral colonies were assessed on each transect. The functional group with the greatest cover in the VRS was crustose coralline algae (mean ± S.E.: 28.9% ± 1.97), stony corals had the second highest cover (21.5% ± 1.24). The Jamapa river divides the VRS into two groups the Veracruz group to the North and the Anton Lizardo group to the south of the river mouth. The Veracruz group had lower crustose coralline algae cover (28.1% ± 2.71) and coral cover (17.8% ± 1.55) than the Anton Lizardo group (29.6% ± 2.87 CCA and 25.3% ± 1.86 coral cover). The highest average coral cover on a reef was recorded at Ahogado Chico (45.5% ± 5.58), and the highest cover recorded on a single transect was 70% at Santiaguillo reef. The lowest coral cover was recorded at the fringing reefs on the north of the VRS, Punta Gorda and Punta Brava which had less than 1% coral cover. Coral colonies averaged 69.1 cm ± 3.10 in length at the VRS, 56.8 cm ± 2.98 in the Veracruz group and 81.7 cm ± 5.11 in the Antón Lizardo group. Old partial mortality was 25% ± 1.05 overall and similar between groups, recent partial mortality was 1.2% ± 0.21 and 1% at both groups. Disease prevalence was 3.9% for the VRS, 2.9% ± 0.88 in the Veracruz group and 4.9% ± 1.11 in the Antón Lizardo group. Overall, these reefs are faring slightly better than other reefs in the Caribbean having higher coral cover and larger colonies. However, the great variability in the health and condition of these reefs demands added attention and clear management goals to ensure their persistence in the face of ever growing threats. It is important to decrease the sources of stress, such as construction and poor waste water management in the area, better regulate fishing and approach a watershed wide management plan which takes into account upstream effects from the rivers that discharge into the Veracruz Reef System.

Key Largo woodrats are an endangered subspecies with an extremely limited habitat. This study sought to understand woodrat habitat preferences in order to guide management. Woodrats build stick nests from natural and artificial materials, so nest distribution and nest occupancy were used as indicators of preference. Distribution was determined by nest surveys, and remote cameras were used to assess occupancy. Forest structure, human disturbance, nest, and animal presence metrics were also collected. More nests were found along abandoned roads than along forest transects and more artificial nests were occupied than natural nests. These findings indicate that woodrats prefer areas with human disturbance, rather than forest age and structure as previously believed. This may have consequences on woodrat management, as it suggests that man-made materials are currently needed by woodrats even in a protected natural area.

Community forestry is an evolving approach to forest management, shown to maintain forest cover, while generating income for local communities. In Sierra Norte (SN), a region with no public protected areas, indigenous communities have been actively conserving their forests for decades, through conservation zoning and careful management of their logging areas. This study found that across 22 communities in SN, an estimated 2,949,116.50 m3 of timber were produced from 1993 to 2013, while the region maintains 78% forest cover. About 75% of the forest is under some form of community conservation. Community governance plays a major role, as rules and regulations regarding use, access, and conservation of communal lands are established and enforced by community members. The findings of this study support arguments that advocate for community forest management, as forest communities prove to maintain forest cover and decrease degradation, thus reducing greenhouse gas emissions and enhancing forest carbon stocks.