Subspecific taxonomic designations solely based on morphological characters can often lead to erroneous assumptions about the evolutionary history of populations. This study sought to investigate evolutionary questions and conservation implications associated with morphological subspecific designations of island populations. To this end, I focused my attention on the Lower Keys of Florida, a unique chain of islands with well-known geologic history and rich in endemic, endangered subspecies. I employed genetic analyses to evaluate historical variation and contemporary restriction of gene flow between the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) and its sister mainland taxa. A Bayesian phylogeny using 1063 base pairs of the mitochondrial cytochrome b gene did not recover reciprocal monophyly of the three named subspecies, and a 95% statistical parsimony haplotype network showed haplotypes being shared among subspecies. Furthermore, clustering analyses using 10 microsatellite loci identified a break within the Lower Keys, separating the western Lower Keys from the island of Big Pine Key. Surprisingly, Big Pine Key grouped with mainland populations and exhibits higher genetic diversity than the western Lower Keys islands. These unexpected findings suggest either a stepping-stone colonization pattern or recent gene flow between the mainland and Big Pine Key via natural dispersal or undocumented man-mediated transfers. Although these results suggest that subspecies designations within S. palustris are unwarranted, this study supports the designation western Lower Keys population as a discrete unit of conservation with regard to both DPS and ESU criteria. The importance of using several lines of evidence to uncover the evolutionary history of populations and implications for the conservation of island populations are discussed.

Genetic variation was examined in bluehead wrasse, Thalassoma bifasciatum, populations along the Florida Keys. Interpretion of mean heterozygosity (H), percent polymorphic loci per population (P), genetic similarity, and F and G statistics demonstrated a clear division of wrasse populations into "northern" and "southern" groups. Correlation and cluster analyses indicated the six reefs can be grouped in a similar fashion based on genetic and environmental data. The conclusion from this analysis of wrasse populations in the Florida Keys is that substantial population subdivision occurs in response to differing selective pressures created by heterogeneous environments.

Understanding the effect of food abundance on feeding behavior can benefit conservation efforts in many ways, such as to determine whether impacted environments need food supplementation, whether different locations of threatened species contain different food abundances, or whether reintroduction sites are missing key components of a species’ diet. I studied the relationship between feeding behavior and food abundance in the Lower Keys marsh rabbit (Sylvilagus palustris hefneri), an endangered subspecies endemic to the lower Florida Keys. Specifically, my study set out to measure the relative abundance of the primary plants within the natural habitat of the Lower Keys marsh rabbit and estimate the proportion of each of these plants within the rabbit’s diet. With this information, I tested the following hypotheses: first, the Lower Keys marsh rabbit selectively feeds on specific plants; second, that diet does not differ among sites; and third, that diet is not affected by food abundance. Using stable isotope analysis, I determined that two plants were prominent in the rabbit’s diet: a shrub, Borrichia frutescens, and a grass, Spartina spartinae. These two species were prominent in the rabbit’s diet in most patches, even where they were relatively rare, suggesting the rabbits are indeed selectively feeding on these species. In addition, although diet did differ among patches, selective feeding was apparent in all cases. Overall, this study determined that certain food types are important food sources for the federally endangered Lower Keys marsh rabbit and that these rabbits do not feed on plants based on plant abundance. This knowledge can be directly applied to reintroduction and restoration efforts for the Lower Keys marsh rabbit. More generally, the methods used in this study can be applied to other species of concern in order to address questions associated with diet requirements and foraging behavior.

Coral reef degradation has been observed worldwide over the past few decades resulting in significant decreases in coral cover and abundance. However, there has not been a clear framework established to address the crucial need for more sophisticated understanding of the fundamental ecology of corals and their response to environmental stressors. Development of a quantitative approach to coral population ecology that utilizes formal, well established principles of fishery systems science offers a new framework to address these issues. The goal of this dissertation is to establish a quantitative foundation for assessment of coral reefs by developing some essential ecological and population-dynamic components of a size-structured demographic model for coral populations of the Florida Keys coral reef ecosystem. The objective provides the potential to build a quantitative systems science framework for coral populations. A two-stage stratified random sampling design was implemented during two separate survey periods to assess coral populations. Results include precise estimates of adult (> 4 cm) population abundance for several coral species by spatially partitioning abundance and variance into species-relevant reef habitat types. Adult size structure and juvenile abundance were used to evaluate individual coral populations and infer spatial variation in recruitment, growth and survival across habitat types. Partial mortality was characterized in terms of surface area, prevalence, and size-relationships. The development of some ecological and population-dynamic components of a size-structured demographic model for coral populations demonstrates the statistical framework and metrics required for monitoring and assessment of coral reef ecosystems to meet the pressing needs of conservation of coral reef ecosystems specifically in Florida, and throughout the Caribbean and Pacific in general.

Multi-beam bridges made from precast concrete box girders are one of the most common bridge types used in the United States. One problem that affects these bridges is the development of longitudinal or reflective cracks on the road surface because of failure of the shear keys. Some states have attempted to correct this problem by redesigning the shear key or adding post-tensioning, but the problem persists in many new bridges. The purpose of this study is to investigate why these shear key failures are occurring. This project studies two types of box girder designs, the common Precast/Prestressed Concrete Institute (PCI) box girder bridges and the Texas Department of Tranportation (TxDOT) box girder bridge. In the past, reflective cracking has occurred in bridges of both types. The analysis procedure involves finite element analyses of bridge models with realistic support and loading conditions, and comparing the PCI and TxDOT bridges. The results indicate that both PCI and TxDOT box girder have sufficient strength to resist cracking from vehicular loads, but uneven temperature changes and shrinkage strains cause high tensile stresses in the shear key regions and lead to reflective cracking. The analyses showed the highest stresses were often times near the supports, rather than at midspan. Past studies have proposed using larger composite deck slabs, transverse posttensioning, or full-depth shear keys to prevent shear key failure. Composite slabs were the most effective way to reduce high stresses in shear keys, and were effective for all loading cases considered. Post-tensioning and full-depth keys also showed a reduction in shear key stresses, but were less effective.

In historical cryptography, a cipher key represents a set of rules by which we can convert between plaintext and ciphertext within an encryption system. Presently, there are not many studies that focus on analysing keys,especially not on a large scale or done in a systematic manner. In this paper, we describe a uniform transcription standard for the keys in the DECODE database. This way, we intend to lay a strong foundation to facilitate further studies on large sets of key transcriptions. We believe that a homogeneous set of transcriptions would be an ideal starting point for comparative studies, especially from a chronological perspective, as this can reveal potential patterns in the evolution of encryption methods. We also build a script that can perform an in-depth analysis of the components of a key, using our standardized transcription files as input. Finally, we give a detailed account of our findings and show that our method can reliably extract valuable information from the transcription file, such as the method of encryption or the types of symbols used for encoding, without the need of additional manual analysis of the original key.

by Amber L. Garr. / Thesis (Ph.D.)--Florida Atlantic University, 2012. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2012. Mode of access: World Wide Web. / The presence of heavy metals and other pollutants is detrimental to marine ecosystems. The queen conch, once an important fisheries species in the Florida Keys, has not sufficiently recovered after a 25-year fishery closure. Research has shown high levels of copper and zinc in the gonads and digestive glands of adult conch found in the nearshore waters. Four sites relevant to queen conch larval recruitment were tested in 2010 for the presence of copper and zinc in the water, phytoplankton, sediment, and seagrass epiphytes over seven months. Both metals were detected in all sample types and no seasonal or geographical differences were detected. Surface water concentrations from the field were used to conduct acute and chronic toxicity tests on various ages of queen conch larvae and their phytoplankton food source. When zinc concentrations (0-40 (So(Bg/L) similar to those measured in situ were used, there was no significant impact on conch larval survival although some velar lobe de velopment was impaired. However, field concentrations of copper (0-15 (So(Bg/L), which often surpassed water quality standards, negatively impacted growth, survival, and development of the larvae. Chronic exposure to copper, through the water and food, disrupted the metamorphic success of competent larvae and decreased post-metamorphosis survival. Exposure to copper at later life stages increased mortality, suggesting that heavy metals have a negative effect on larval recruitment in localized areas of the Florida Keys. Structural equation modeling revealed that copper and zinc are moving through the systems differently and are best represented by two different models.

Title from PDF of title page. / Document formatted into pages; contains 112 pages. / Thesis (M.S.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: The Florida Keys Coral Reef Monitoring Project (CRMP) began video transect sampling in 1996 and has continuously monitored 107 Florida Keys stations through 2002. The video was downward pointing and produced images from which planar projection data were calculated to determine percent cover of living benthic organisms. An absence of data assessing correlation between octocoral percent cover and octocoral abundance motivated a study to compare octocoral percent cover with abundance data acquired from the same video transects. The methods employed to extract octocoral abundance data from videotape were validated. Temporal changes in octocoral abundance, size and taxonomic group were determined by examination of video transects of 28 randomly selected stations from 1996, 1998, 1999, and 2002. Size classes were defined as [10cm, 10-40cm, ]40cm (short, medium and tall respectively). / ABSTRACT: Taxonomic groups were Gorgonia ventalina and "other octocorals" in three size classes, and Scleraxonia. An in situ study assessed the accuracy of video-derived counts. Average densities of G. ventalina and Scleraxonia were consistently about one colony/m2. Other octocoral as a group averaged 7-9 colonies/m2. When summarized by height, short and tall averaged about 1-2 colonies/m2, while colonies between 10 and 40 cm in height consistently averaged about 6 colonies/m2. Hurricane Georges, in September 1998, impacted the octocoral assemblage. Abundance declined most at stations near the storm center and stations in shallower water. Storm impact was related to octocoral height. Tall octocorals were removed more frequently than medium, short and encrusting forms. A dramatic increase of short individuals in 2002 is indicative of successful post-hurricane recruitment. By 2002, octocoral abundance had recovered to pre-hurricane levels. / ABSTRACT: This study demonstrated that abundance data can reliably be derived from archived video data, reinforcing the value of standardized video data archives. Octocoral abundance and octocoral percent cover are not strongly correlated because tall individuals disproportionately influence percent cover estimates. Nevertheless, trends in octocoral percent cover are reliable indicators of the trends in octocoral abundance. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Environmental variation is ubiquitous in natural systems. The genetic and physiological mechanisms governing population-level responses to this variation will impact the process of speciation and the capacity for populations to persist in a changing climate. Until recently, population-level responses to environmental selection remained largely unexplored in marine systems due to the historical assumption that the inherently dispersive nature of most marine taxa would preclude their ability to specialize to local environments. This dissertation represents the first investigation of population-level responses to environmental variation in a Caribbean reef-building coral. This research integrates ecological, physiological, genetic and genomic methods to (1) determine patterns of local adaptation in the Florida Keys, (2) identify stressors driving adaptive responses, (3) distinguish the physiological and genetic mechanisms underlying coral adaptation and (4) assess the potential for future adaptation in the common reef-building coral Porites astreoides. Results demonstrate that corals adapt and/or acclimatize to their local habitat and that this specialization incurs fitness costs. Temperature differences between reefs likely play a selective role in differentiating inshore and offshore coral populations. Genetic and gene expression differences indicate that coral hosts play a substantial role in driving these population-level differences. Inshore corals exhibit greater gene expression plasticity, which may be involved in stabilizing physiological responses to temperature fluctuations experienced at inshore reefs. In addition, naïve juvenile coral recruits from inshore reefs exhibit a growth rate advantage over offshore recruits under elevated temperature treatment, suggesting that thermotolerance differences observed in adult populations could continue to evolve in response to climate change. Taken together these results provide novel insight into the drivers of reef decline in the Florida Keys and the role of the host in coral adaptation capacity. / text

As espécies da subfamília Astrodoradinae foram revisadas e uma análise filogenética conduzida. Foram reconhecidas 21 espécies distribuídas em sete gêneros. Acanthodoras e Agamyxis, outrora considerados próximos a Platydoras foi considerado sinônimo ju nior de A. weddellii e uma nova espécie é descrita do alto Araguaia. Os gêneros Merodoras e Physopyxis foram considerados sinônimos A. ananas, A. bolivarensis, A. cristatus, A. lyra e A. nheco. Duas novas espécies de Astrodoras são reconhecidas, ocorrendo sintopicamente com A. asterifrons em alguns lugares da bacia amazônica. Scorpiodoras calderonensis é revalidado e sua localidade tipo elucidada, revelando-se ser Tabatinga. Além disso, uma nova espécie de Scorpiodoras foi descrita no médio rio Madeira. A análise cladística foi feita com base em 101 caracteres codificados para 28 táxons, resultando em uma única árvore mais parcimoniosa com 279 passos. O monofiletismo de Astrodoradinae foi sustentado por sete sinapomorfias não exclusivas: fontanela craniana anterior oval ou circular, número reduzido de costelas (oito ou menos), coracóide não coberto completamente por musculatura ventral, número reduzido de vértebras (34 ou menos), para-hipural fusionado aos hipurais 1 e 2, infra-orbital 1 participando da órbita e terceiro escudo timpânico expandido. Anadoras é considerado o gênero mais basal de Astrodoradinae, seguido por (Acanthodoras + Agamyxis) (Amblydoras (Scorpiodoras (Hypodoras + Astrodoras))). / The species of the subfamily Astrodoradinae was revised and a phylogenetic analysis performed. Twenty-one species, belonging to seven genera, are recognized as valid. Acanthodoras and Agamyxis, formely considered to be related to Platydoras,are included into Astrodoradinae. Anadoras regani is considered as a junior synonym of A. weddellii and a new species is described from the upper Araguaia. The genera Merodoras and Physopyxis are placed in synonym with Amblydoras,which has six valid species: A. affinis, A. ananas, A. bolivarensis, A. cristatus, A. lyra and A. nheco.Two new species of Astrodoras are described and occur syntopically in some places in the Amazon basin. Scorpiodoras calderonensis is reerected and its type locality elucidated as Tabatinga. Furthermore, a new species of Scorpiodoras is discribed from the middle rio Madeira. The cladistic analysis was performed based on 101 characters coded for 28 taxa and resulted in a single most parcimonious tree with 279 steps. The monophyly of Astrodoradinae is supported by seven non-exclusive synapomorphies: anterior cranial fontanel oval or circular, reduced number of ribs (eigth or less), ventral face of coracoid not completely covered by muscles, reduced number of vertebrae (34 or less), parhypural fused to hipural 1 and 2, infra-orbital 1 participating of orbit and third tympanic scute expanded. Anadoras is considered the most basal genus of Astrodoradinae, followed by (Acanthodoras + Agamyxis)(Amblydoras (Scorpiodoras (Hypodoras + Astrodoras))).