Recent improvements in genetic analyses have paved the way in using molecular data to answer questions regarding evolutionary history, genetic structure, and demography. Key deer are a federally endangered subspecies assumed to be genetically unique (based on one allozyme study), homogeneous, and have a female-biased population of approximately 900 deer. I used 985bp of the mitochondrial cytochrome b gene and 12 microsatellite loci to test two hypotheses: 1) if the Moser Channel is a barrier to gene flow, I should expect that Key deer are differentiated and have reduced diversity compared to mainland deer and (2) if isolation on islands leads to a higher probability of extinction, I should expect that Key deer exhibit a small population size and a high risk of extinction. My results indicate that Key deer are genetically isolated from mainland white-tailed deer and that there is a lack of genetic substructure between islands. While Key deer exhibit reduced levels of genetic diversity compared to their mainland counterparts, they contain enough diversity of which to uniquely identify individual deer. Based on genetic identification, I estimated a census size of around 1,000 individuals with a heavily skewed female-biased adult sex ratio. Furthermore, I combined genetic and contemporary demographic data to generate a species persistence model of the Key deer. Sensitivity tests within the population viability analysis brought to light the importance of fetal sex ratio and female survival as the primary factors at risk of driving the subspecies to extinction.

Wildlife biologists and land managers tasked with the recovery of the endangered Lower Keys marsh rabbit (LKMR; Sylvilagus palustris hefneri) were in need of a current population estimate as well as a method to estimate the LKMR population annually. Habitat loss and fragmentation from population growth and development have threatened the existence of the LKMR. Establishing and understanding long-term habitat availability for the LKMR is important for determining causes of historical population declines as well as designing and implementing successful recovery plans. I conducted a range-wide pellet survey and a mark-recapture study to estimate the LKMR population. I evaluated the fit of 5 models and considered the variation in behavioral response model the best model. I correlated (r2 = 0.913) this model's rabbit abundance estimates to pellet density in 11 patches and generated a range-wide population estimate of 317, a western clade population of 257, an eastern clade population of 25, and translocated LKMR populations of 35 and 0 on Little Pine and Water keys, respectively. This prediction equation provides managers a quick, efficient, and non-invasive method to estimate LKMR abundance from pellet counts. To quantify the amount of habitat loss and fragmentation that occurred over the last 50 years, I systematically delineated and compared potential LKMR habitat using 1959 and 2006 aerial photographs. Additionally, I investigated if other factors could have reduced the amount of suitable habitat available for the LKMR with a comparison of habitat loss and fragmentation on a developed island and an undeveloped island. Range-wide, I found that number of habitat patches increased by 38, total class area decreased by 49.0%, and mean patch size decreased by 44.3%. Mean shape index increased by 4.2% and mean proximity index decreased by 13%. Both the 1959 and 2006 connectance indices were low while the 2006 set decreased 12.1%. I observed the same patterns of habitat loss and fragmentation on both the developed and undeveloped islands as I did in the range-wide landscape analysis. I found that LKMR habitat has declined in area and become more fragmented over the last 50 years. Habitat loss and fragmentation by development have directly endangered the LKMR; however, sea level rise and woody encroachment also could have historically caused habitat loss and fragmentation. Although development in LKMR habitat was halted, sea-level rise and woody encroachment could continue to alter LKMR habitat.

The time-honored profession of commercial fishing in the Florida Keys is in danger of extinction as each year passes and fewer commercial fishermen remain in an industry that is sinking in the wake of politicians, land developers, and financial woes. At the heart of the problem is the threat of overfishing, a subject that is increasingly at the forefront of media attention and environmental campaigns. The villain in this story of death and destruction more often than not are commercial fishermen. But the blame is misguided. Our fishermen work according to the letter of the law and strive to maintain healthy sustainable fish stocks and sound marine ecosystems. It is unlikely that the American hunger for seafood will diminish so in the absence of locally caught fish the public has no choice but to support the efforts of unchecked foreign fisheries—Fisheries that are not managed as well as ours and in some instances fish until there is nothing left to take. / text

Over the last 40 years, the Caribbean has lost half of its live coral cover, mostly in the form of Acropora cervicornis and A. palmata, due to disease, bleaching from rising water temperatures, and other stressors. To help restore these corals to reefs in Florida, the Coral Restoration Foundation (CRF) created nearshore nurseries and transplanted over 30,000 acroporid colonies across the Florida Keys. The objective of this thesis was to evaluate the growth, survivorship, and condition of nursery-raised A. cervicornis colonies that were part of two transplant projects: 1) photographic analyses of 17 past CRF transplant projects over the last seven years; and 2) a transplant experiment at Little Conch Reef to additionally assess the effects of depth, colony density, and the genetic composition of transplants. The photographic analyses included 2,428 individual colonies, 38 genotypes, and six reefs from 2007 to 2013. Results from the photographs were combined with one in situ monitoring effort that used SCUBA in 2014. In the Little Conch Reef experiment, 1,288 colonies from 14 genotypes were transplanted in October and November, 2013 at two depths (5m and 12m) in either cluster or thicket configurations. At each depth, clusters comprised 14 colonies, each placed within in 1m diameter radius, with ten monogenetic and six multigenetic structures. Thickets were 3.5m by 1.5m in size, with 10 colonies from each genotype forming its own subunit within the larger configuration. In June 2014, 963 additional colonies were added to the shallow site by stacking them on top of six existing clusters and one thicket to evaluate whether larger three-dimensional structures affected growth or survival. The Little Conch Reef experiment was monitored through January 2015. Results from the photographic analyses were: 1) maximum size of A. cervicornis transplants was approximately 40cm in diameter; 2) mortality increased after approximately two years; 3) despite high mortality, some colonies survived the duration of each project; and 4) frequent and long-term monitoring is required to assess factors that affect survival and condition. Results from the Little Conch Reef experiment suggest: 1) maximum skeletal diameter was unaffected by any of the treatments; 2) percent survival and percent live tissue were higher at the shallow site compared to the deep site, and similarly, the clusters outperformed the thickets, and multigenetic clusters outperformed their monogenetic counterparts; 3) location within the shallow site had an impact on survival and condition, with clusters doing better on the south side than on the north; and 4) stacking did not positively impact growth, survival, or condition. In general, the sizes and condition of natural populations of A. cervicornis throughout the Florida Keys are similar to results from both experiments and with other transplant projects conducted in the Caribbean. Remarkably, despite high mortality in nearly all of the projects, small numbers of colonies transplanted for most projects, a few colonies survived to 2014/2015. These colonies have the potential to act as a “seed population” that might produce sexually dispersed larvae better adapted at surviving mortality events and asexual fragments that may be better acclimated to the stressors related to their location. Evidence of persistence in this species and expansion northward in Florida suggest that it is too early to consider coral reefs a lost cause, and that coral restoration holds promise for enhancing recovery of A. cervicornis.

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.

Located 100 km west of Key West, Florida, Dry Tortugas National Park (DRTO) is a largely untouched subtropical marine ecosystem that serves as an important developmental habitat, nesting ground, and foraging area for several species of sea turtles, including green turtles. The Park supports a recovering population of green turtles comprised of resident juveniles, subadults, and adults of both sexes; nesting females include residents and migrating females that only return to nest. Stable isotope analysis has been applied widely to describe the trophic ecology of green turtles, from urbanized bays with significant anthropogenic input, to relatively pristine ecosystems with healthy populations at carrying capacity. However, there is a paucity of published literature about the trophic ecology of green turtles in DRTO. This study describes the trophic ecology occupied by two distinct size groups (61 green turtles < 60 cm (SCL) and 98 green turtles > 60 cm (SCL)). Flipper tissue and plasma were analyzed for stable isotopic composition of C and N. Flipper tissue values for δ15N (3.41‰ to 9.69‰) and δ13C (-22.43‰ to -5.38‰) fall within literature values for green turtles, and the wide range of values indicated they could potentially feed at multiple trophic levels. Understanding the trophic ecology of this population of green sea turtles is instrumental to effective management and habitat preservation strategies in DRTO.

The sea-surface microlayer (SML) is the boundary layer at the air-sea interface where many biogeochemical processes occur. Many organisms (e.g., bacteria) produce surface active agents (surfactants) for life processes, which accumulate in the SML and dampen short gravity-capillary waves, resulting in sea surface slicks. Synthetic aperture radar (SAR) is capable of remotely sensing these features on the sea surface by measuring reflected backscatter from the ocean surface in microwaves. This study coordinates SAR overpasses with in situ SML and subsurface (SSW) microbial sample collection to guide subsequent analysis after 16s rRNA sequencing on the Illumina MiSeq. In April 2017, 138 SML and SSW samples were collected near a targeted oil-seep where the Taylor Platform was knocked down in the Gulf of Mexico, both in and out of visually-observed oil slicks. In July and August 2018, 220 SML and SSW samples were collected near the Looe Key coral reef and a coastal seagrass area. Analysis of microbial abundance and diversity between the two experiments shows that within oil slicks, surfactant- and oil-associated bacteria prefer to reside within the SSW rather than in the SML. In natural slicks in the coastal seagrass area, these bacteria are more abundant in the SML. Outside of these slicks, surfactant-associated bacteria are more abundant within the SML than the SSW. This suggests that the presence of oil reduces the habitability of the SML, whereas natural slicks created by foam and other surfactants creates a more habitable environment in the SML. With lower wind speed, abundance of these bacteria are greater, as increased wind speed results in a harsher environment. The diurnal cycle had an effect on the relative abundance of surfactant-associated bacteria in the SML and SSW. Our results demonstrate the usefulness of synthetic aperture radar to remotely sense sea surface slicks in coordination with in situ surfactant-associated bacteria data collection of the sea surface slicks.

Coastal forest retreat in the Florida Keys during the 20th century has been attributed to a combination of sea level rise and hurricane storm surge impacts, but the interactions between these two disturbances leading to forest decline are not well understood. The goal of my research was to assess their effects over a period spanning more than two decades, and to examine the relationships between these press and pulse disturbances and freshwater availability in pine rockland, hardwood hammock, and supratidal scrub communities. Impacts and recovery from two storm surges, Hurricanes Georges (1998) and Wilma (2005), were assessed with satellite-derived vegetation indices and multiple change detection techniques. Impacts were greater at lower elevations, and in hardwood hammock, spectral signatures indicative of plant stress and productivity returned to pre-disturbance levels within a few years. In pine rockland, impacts were predominately related to Hurricane Wilma, however, a similar return to pre-disturbance conditions was absent, suggesting that trajectories of disturbance recovery differed between the two communities. Long-term monitoring of forest composition, structure, and groundwater salinity showed that compositional shifts in the low shrub stratum were associated with salinization of the freshwater resource attributable to sea level rise. Throughout the course of twelve months of climate and groundwater monitoring (2011-2012), groundwater salinity generally decreased in response to large precipitation events. Modeling of geophysical data indicated that groundwater salinity was an important predictor of community type. Isotopic analysis of d18O in plant stem water and foliar d13C was used to determine temporal and spatial patterns in water use and plant stress in two community dominants, slash pine, Pinus elliottii var. densa, and buttonwood, Conocarpus erectus. Both species relied heavily on groundwater, and plant stress was related to increasing groundwater salinity. The results of this work suggest that the interaction of press and pulse disturbances drive changes in community composition by causing mortality of salt-sensitive species and altering the freshwater resource.