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- Title
- HISTORICAL RESPONSES OF MARINE TURTLES TO GLOBAL CLIMATE CHANGE AND JUVENILE LOGGERHEAD RECRUITMENT IN FLORIDA.
- Creator
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Reece, Joshua, Parkinson, Christopher, University of Central Florida
- Abstract / Description
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Marine turtle conservation is most successful when it is based on sound data incorporating life history, historical population stability, and gene flow among populations. This research attempts to provide that information through two studies. In chapter I, I identify historical patterns of gene flow, population sizes, and contraction/expansion during major climatic shifts. In chapter II, I reveal a life history characteristic of loggerhead turtles previously undocumented. I identify a pattern...
Show moreMarine turtle conservation is most successful when it is based on sound data incorporating life history, historical population stability, and gene flow among populations. This research attempts to provide that information through two studies. In chapter I, I identify historical patterns of gene flow, population sizes, and contraction/expansion during major climatic shifts. In chapter II, I reveal a life history characteristic of loggerhead turtles previously undocumented. I identify a pattern of juvenile recruitment to foraging grounds proximal to their natal nesting beach. This pattern results in a predictable recruitment pattern from juvenile foraging ground aggregations to local rookeries. This research will provide crucial information to conservation managers by demonstrating how sensitive marine turtles are to global climate change. In the second component of my research, I demonstrate how threats posed to juvenile foraging grounds will have measurable effects on rookeries proximal to those foraging grounds. The addition of this basic life history information will have dramatic effects on marine turtle conservation in the future, and will serve as the basis for more thorough, forward-looking recovery plans.
Show less - Date Issued
- 2005
- Identifier
- CFE0000341, ucf:46281
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0000341
- Title
- MODELING AND PARTITIONING THE NUCLEOTIDE EVOLUTIONARY PROCESS FOR PHYLOGENETIC AND COMPARATIVE GENOMIC INFERENCE.
- Creator
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Castoe, Todd, Parkinson, Christopher, University of Central Florida
- Abstract / Description
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The transformation of genomic data into functionally relevant information about the composition of biological systems hinges critically on the field of computational genome biology, at the core of which lies comparative genomics. The aim of comparative genomics is to extract meaningful functional information from the differences and similarities observed across genomes of different organisms. We develop and test a novel framework for applying complex models of nucleotide evolution to solve...
Show moreThe transformation of genomic data into functionally relevant information about the composition of biological systems hinges critically on the field of computational genome biology, at the core of which lies comparative genomics. The aim of comparative genomics is to extract meaningful functional information from the differences and similarities observed across genomes of different organisms. We develop and test a novel framework for applying complex models of nucleotide evolution to solve phylogenetic and comparative genomic problems, and demonstrate that these techniques are crucial for accurate comparative evolutionary inferences. Additionally, we conduct an exploratory study using vertebrate mitochondrial genomes as a model to identify the reciprocal influences that genome structure, nucleotide evolution, and multi-level molecular function may have on one another. Collectively this work represents a significant and novel contribution to accurately modeling and characterizing patterns of nucleotide evolution, a contribution that enables the enhanced detection of patterns of genealogical relationships, selection, and function in comparative genomic datasets. Our work with entire mitochondrial genomes highlights a coordinated evolutionary shift that simultaneously altered genome architecture, replication, nucleotide evolution and molecular function (of proteins, RNAs, and the genome itself). Current research in computational biology, including the advances included in this dissertation, continue to close the gap that impedes the transformation of genomic data into powerful tools for the analysis and understanding of biological systems function.
Show less - Date Issued
- 2007
- Identifier
- CFE0001548, ucf:47138
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001548
- Title
- WIKIPDF - A TOOL TO HELP SCIENTISTS UNDERSTAND THE LITERATURE OF THE BIOLOGICAL, HEALTH, AND LIFE SCIENCES.
- Creator
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Calloway, David, Parkinson, Christopher, University of Central Florida
- Abstract / Description
-
Biological sciences literature can be extraordinarily difficult to understand. Papers are commonly filled with terminology unique to a particular sub-discipline. Readers with expertise outside that sub-discipline often have difficulty understanding information the author is trying to convey. The WikiPDF project that is the subject of this thesis helps readers understand the biological sciences literature by automatically generating a customized glossary for each page of any technical paper...
Show moreBiological sciences literature can be extraordinarily difficult to understand. Papers are commonly filled with terminology unique to a particular sub-discipline. Readers with expertise outside that sub-discipline often have difficulty understanding information the author is trying to convey. The WikiPDF project that is the subject of this thesis helps readers understand the biological sciences literature by automatically generating a customized glossary for each page of any technical paper available in Adobe Portable Document Format (PDF) format. WikiPDF relies on the Wikipedia®, an on-line encyclopedia created and supported by a host of volunteers, as a source of definitions used in its glossaries. WikiPDF uses the National Institutes of Health (NIH) Medline/PubMed database of journal papers to organize, index, and locate WikiPDF glossaries. Design and implementation of this project relied exclusively on open-source software, including the Linux operating system, the Apache Tomcat web server, and the MySQL relational database system.
Show less - Date Issued
- 2006
- Identifier
- CFE0001084, ucf:46782
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001084
- Title
- BIOGEOGRAPHY AND DIVERSIFICATION IN THE NEOTROPICS: TESTING MACROEVOLUTIONARY HYPOTHESES USING MOLECULAR PHYLOGENETIC DATA.
- Creator
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Daza Rojas, Juan Manuel, Parkinson, Christopher, University of Central Florida
- Abstract / Description
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Lineage diversification in the Neotropics is an interesting topic in evolutionary biology and one of the least understood. The complexity of the region precludes generalizations regarding the historical and evolutionary processes responsible for the observed high diversity. Here, I use molecular data to infer evolutionary relationships and test hypotheses of current taxonomy, species boundaries, speciation and biogeographic history in several lineages of Neotropical snakes. I comprehensively...
Show moreLineage diversification in the Neotropics is an interesting topic in evolutionary biology and one of the least understood. The complexity of the region precludes generalizations regarding the historical and evolutionary processes responsible for the observed high diversity. Here, I use molecular data to infer evolutionary relationships and test hypotheses of current taxonomy, species boundaries, speciation and biogeographic history in several lineages of Neotropical snakes. I comprehensively sampled a widely distributed Neotropical colubrid snake and Middle American pitvipers and combined my data with published sequences. Within the colubrid genus Leptodeira, mitochondrial and nuclear markers revealed a phylogeograhic structure that disagrees with the taxonomy based only on morphology. Instead, the phylogenetic structure corresponds to specific biogeographic regions within the Neotropics. Molecular evidence combined with explicit divergence time estimates reject the hypothesis that highland pitvipers in Middle America originated during the climatic changes during the Pleistocene. My data, instead, shows that pitviper diversification occurred mainly during the Miocene, a period of active orogenic activity. Using multiple lineages of Neotropical snakes in a single phylogenetic tree, I describe how the closure of the Isthmus of Panama generated several episodes of diversification as opposed to the Motagua-Polochic fault in Guatemala where a single vicariant event may have led to diversification of snakes with different ecological requirements. This finding has implications for future biogeographic studies in the region as explicit temporal information can be readily incorporated in molecular clock analyses. Bridging the gap between the traditional goals of historical biogeography (i.e., area relationships) with robust statistical methods, my research can be applied to multiple levels of the biological hierarchy (i.e., above species level), other regional systems and other sub-disciplines in biology such as medical research, evolutionary ecology, taxonomy and conservation.
Show less - Date Issued
- 2010
- Identifier
- CFE0003101, ucf:48328
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003101
- Title
- CLONALITY AND GENETIC DIVERSITY IN POLYGONELLA MYRIOPHYLLA, A LAKE WALES RIDGE ENDEMIC PLANT.
- Creator
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Metzger, Genevieve, Parkinson, Christopher, University of Central Florida
- Abstract / Description
-
Although capable of sexual reproduction, many plants also rely heavily on clonal reproduction. The formation of multiple, physiologically-independent units with the same genotype has important implications for spatial genetic structure and genetic diversity in these plants. The endangered scrub-dwelling perennial, Polygonella myriophylla is known to reproduce both sexually and clonally but no study to date has been able to investigate the spatial genetic patterns that occur in this species. I...
Show moreAlthough capable of sexual reproduction, many plants also rely heavily on clonal reproduction. The formation of multiple, physiologically-independent units with the same genotype has important implications for spatial genetic structure and genetic diversity in these plants. The endangered scrub-dwelling perennial, Polygonella myriophylla is known to reproduce both sexually and clonally but no study to date has been able to investigate the spatial genetic patterns that occur in this species. I use microsatellite markers to investigate questions about clonal structure and genetic diversity in five populations of P. myriophylla and address some of the implications of my findings for conservation of this species: Overall, I find that 57% of sampled clusters of P. myriophylla are composed of a single genet (genetic individual) with multiple physiological units (ramets) while the remainder are made up of two or more genets. I found differences in both clonal reproduction and genetic diversity among populations. I also found evidence of limited gene flow even over small spatial scales (less than 10 km) and for at least 4 genetic clusters occurring within the species range. Despite high levels of genetic diversity overall, there is evidence of reduced genetic diversity in two populations My results suggest that high levels of clonality may be important in maintaining genetic diversity in P. myriophylla. I also provide evidence that dirt roadsides may not represent a refuge for this species.
Show less - Date Issued
- 2010
- Identifier
- CFE0003264, ucf:48516
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003264
- Title
- Unearthing the past and present of a semi-fossorial lizard: conservation genetics, phylogeography, and taxonomy of Plestiodon egregius.
- Creator
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Mercier, Kathryn, Savage, Anna, Parkinson, Christopher, Jenkins, David, University of Central Florida
- Abstract / Description
-
Characterizing an organism's evolutionary history and population structure as well as understanding the forces shaping that divergence is crucial to conservation biology. A clear understanding of the patterns of diversity and divergence are imperative for the best management ofthe organism, while an awareness of what drives these patterns can lead to better predictions of how organisms will respond to future climate change. Historical climate changes and associated sea levelchange are among...
Show moreCharacterizing an organism's evolutionary history and population structure as well as understanding the forces shaping that divergence is crucial to conservation biology. A clear understanding of the patterns of diversity and divergence are imperative for the best management ofthe organism, while an awareness of what drives these patterns can lead to better predictions of how organisms will respond to future climate change. Historical climate changes and associated sea levelchange are among the main forces driving divergence in many species. To examine how effects of climate changes may have driven patterns of intraspecific divergence, I examined Mole Skinks,Plestiodon egregius, a semi-fossorial lizard of conservation concern. First, I characterized P. egregius evolutionary history and population structure using multiple data sources: morphological characters,mitochondrial sequences (mtDNA), and genome-wide single nucleotide polymorphisms (SNPs). I determined that SNP data distinguished population structure at a finer resolution than morphologyor mtDNA. From these data, I defined six conservation units within P. egregius, three of which are consistent with current subspecific taxonomy. Next, I used statistical phylogeography to examinehow the effects of historical climate change in the southeastern United States (US) may have driven patterns of intraspecific divergence in P. egregius. I devised a set of alternative hypotheses regardingthe historical distribution and dispersal of P. egregius to test using genome-wide SNP markers. I found support for a historical refugia within the southern scrub ridges in Florida followed byexpansion into the Florida peninsula and mainland US. Synthesizing the results from both studies, I evaluate the current subspecific taxonomy and discuss the conservation of P. egregius. Overall, Iconclude that P. egregius evolutionary history has been driven by historical sea level changes in the southeastern US, and that insular populations should be the focus of conservation efforts.
Show less - Date Issued
- 2018
- Identifier
- CFE0007225, ucf:52228
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007225
- Title
- Beyond building a tree: Phylogeny of pitvipers and exploration of evolutionary patterns.
- Creator
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Fenwick, Allyson, Parkinson, Christopher, Hoffman, Eric, Crampton, William, Wiens, John, University of Central Florida
- Abstract / Description
-
As generic and higher-scale evolutionary relationships are increasingly well understood, systematists move research in two directions: 1) understanding species-level relationships with dense taxon sampling, and 2) evaluating evolutionary patterns using phylogeny. In this study I address both foci of systematic research using pitvipers, subfamily Crotalinae. For direction one, I evaluate the relationships of 96% of pitvipers by combining independent sets of molecular and phenotypic data. I...
Show moreAs generic and higher-scale evolutionary relationships are increasingly well understood, systematists move research in two directions: 1) understanding species-level relationships with dense taxon sampling, and 2) evaluating evolutionary patterns using phylogeny. In this study I address both foci of systematic research using pitvipers, subfamily Crotalinae. For direction one, I evaluate the relationships of 96% of pitvipers by combining independent sets of molecular and phenotypic data. I find the inclusion of species with low numbers of informative characters (i.e. less than 100) negatively impacts resolution of the phylogeny, and the addition of independent datasets has no effect on or a small benefit to confidence in estimated evolutionary relationships. Combined evidence is extremely useful in evaluating taxonomy; I use it with South American bothropoid pitvipers. Previous work found the genus Bothrops paraphyletic, but no study had included enough species to propose a taxonomic resolution. I resolve the relationships of 90% of bothropoid pitvipers, and support the paraphyly of Bothrops as previously defined, but find it consists of three well-supported clades distinguished by distinct habitats and geographic ranges. I propose the division of Bothrops sensu lato into three genera.To address research direction two, I investigate the change in reproductive mode from egg-laying (oviparity) to livebearing (viviparity) in vipers, as well as the expansion of pitvipers through South America. I resolve the phylogeny and the divergence times for subgroups of interest then use model comparison and ancestral character state or geographic range estimation to trace the evolution of reproductive mode or geographic range across evolutionary history. For vertebrates, the predominant explanation for the evolution of reproductive mode is Dollo's Law of unidirectional evolution. This law has been challenged for a number of characters in different systems, but the phylogenetic methods that found those violations were criticized. I find support for unidirectional evolution in two analyses and rejection of it in others, and therefore do not reject Dollo's Law for the evolution of reproductive mode in vipers. In the case of geographic range, dozens of hypotheses have been proposed to explain the great biodiversity in South America, but tests of these hypotheses are lacking. I define specific time- and space-based predictions for seven hypotheses based on geological and climatic events (-) uplift of the Andes Mountains, saltwater inundation of inland areas, change in river flow, and Pleistocene climate changes. I find some support for half of the hypotheses, including one allopatric, one parapatric, and one based on climate change. I conclude that the evolution of South American pitvipers is extremely complex. Through fulfillment of both systematic research directions, I generated new knowledge about pitvipers and evolutionary processes. My methods of evaluating evolutionary patterns provide frameworks for different research questions in these areas, and I suggest that other researchers apply similar techniques to evaluate other portions of the Tree of Life.
Show less - Date Issued
- 2012
- Identifier
- CFE0004535, ucf:49236
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004535
- Title
- Indirect estimates of gene flow and conservation implications in the striped newt (Notophthalmus perstriatus).
- Creator
-
May, Sarah, Hoffman, Eric, Parkinson, Christopher, Johnson, Steve, University of Central Florida
- Abstract / Description
-
This study used indirect methods to estimate patterns of gene flow in a rare salamander species, the striped newt (Notophthalmus perstriatus). First, we used combined genetic and ecological methods to determine whether populations that appear to exist in two regions separated by 125 km, exhibited genetic and ecological distinctness such that the regions demarcate separate conservation units. Using mtDNA (cyt-b), we found that haplotypes were shared between localities within each region but...
Show moreThis study used indirect methods to estimate patterns of gene flow in a rare salamander species, the striped newt (Notophthalmus perstriatus). First, we used combined genetic and ecological methods to determine whether populations that appear to exist in two regions separated by 125 km, exhibited genetic and ecological distinctness such that the regions demarcate separate conservation units. Using mtDNA (cyt-b), we found that haplotypes were shared between localities within each region but none were shared between regions. Niche-based distribution modeling revealed significant differences in the ecological setting between the two regions. In combination, the absence of evidence for recent genetic exchange and model-based support for differing ecological conditions utilized by newts between regions provides evidence that eastern and western populations are both distinct and significant. This study suggests a framework to evaluate discreteness and significance among populations for assessment of distinct population segments (DPSs which can be used as a conservation tool for many species. Second, we used microsatellites to characterize patterns of population connectivity, genetic differentiation, and effective population size in N. perstriatus. We assessed these patterns by testing several a priori hypotheses regarding the influence of gene flow and genetic drift on the distribution of genetic variation among and within populations. Interestingly, several of our results did not conform to our hypotheses. For example, our assessment did not reveal a significant pattern of isolation by distance among populations in this study. Additionally, we found that effective population sizes and genetic diversity of isolated populations were higher than expected. We discuss our results relate to our a priori hypotheses and we address the general question of why this species exhibited patterns contrary to what we expected given previous data on this taxon and other studies of similar taxa
Show less - Date Issued
- 2011
- Identifier
- CFE0004481, ucf:49311
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004481
- Title
- Testing for Isolation in Florida Raccoons (Procyon lotor) Using Phylogenetics and Population Genetic Structure.
- Creator
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Trujillo, Alexa, Hoffman, Eric, Fedorka, Kenneth, Parkinson, Christopher, University of Central Florida
- Abstract / Description
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Molecular data are useful in determining if populations are isolated and for species delimitation. Researchers and managers currently recognize five subspecies of raccoons (Procyon lotor) in Florida, based largely on perceived geographic isolation due to the island ranges of four subspecies. In this study, I provide the first estimate of phylogenetic relationships and population divergences within Florida raccoons using a molecular dataset. I analyze the mitochondrial control region,...
Show moreMolecular data are useful in determining if populations are isolated and for species delimitation. Researchers and managers currently recognize five subspecies of raccoons (Procyon lotor) in Florida, based largely on perceived geographic isolation due to the island ranges of four subspecies. In this study, I provide the first estimate of phylogenetic relationships and population divergences within Florida raccoons using a molecular dataset. I analyze the mitochondrial control region, cytochrome b gene, and eight nuclear microsatellite loci to test two hypotheses: 1) the five, morphologically and geographically-defined subspecies of raccoon in Florida represent genetically distinct populations and (2) due to differing range sizes and habitat variation between island and mainland subspecies, the four island populations should exhibit reduced levels of genetic diversity and smaller effective population sizes compared to the mainland population. My results indicate no evidence of historical differentiation between the subspecies, but suggest a recent restriction of gene flow among three clusters of raccoons. The three clusters do not correlate to traditional geographies for subspecies identification. I provide evidence of reduced genetic diversity in island populations of raccoons compared to their mainland counterparts. These data stress the importance of using multiple lines of evidence when naming taxa to avoid misinforming the taxonomy.
Show less - Date Issued
- 2015
- Identifier
- CFE0006233, ucf:51069
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006233
- Title
- Genetic structure and demographic analysis of Key deer (Odocoileus virginianus clavium).
- Creator
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Villanova, Vicki, Hoffman, Eric, Parkinson, Christopher, Fedorka, Kenneth, University of Central Florida
- Abstract / Description
-
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...
Show moreRecent 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.
Show less - Date Issued
- 2015
- Identifier
- CFE0006058, ucf:50981
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006058
- Title
- Assessment of Staphylococcus aureus Genetics: Clinical versus Community Epidemiology.
- Creator
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Lawrance, Matthew, Parkinson, Christopher, Savage, Anna, Cole, Alexander, University of Central Florida
- Abstract / Description
-
Staphylococcus aureus has an historical relationship with anthropogenic environments, particularly hospitals, where infection characteristics differ from community-acquired disease. This has promoted a designation of strains as healthcare or community associated. Despite this affiliation, genetic approaches have failed to support these groupings. In order to establish the genetic relationship between S. aureus from differing anthropogenic environments, I have analyzed the relatedness between...
Show moreStaphylococcus aureus has an historical relationship with anthropogenic environments, particularly hospitals, where infection characteristics differ from community-acquired disease. This has promoted a designation of strains as healthcare or community associated. Despite this affiliation, genetic approaches have failed to support these groupings. In order to establish the genetic relationship between S. aureus from differing anthropogenic environments, I have analyzed the relatedness between three cohorts of S. aureus: nasal carriage isolates from community participants, infectious isolates from hospitals, and a cohort from an uninvestigated environment, an ambulatory clinic. Multilocus Sequence Typing (MLST) and Staphylococcus aureus protein a (spa) repeat regions were analyzed and the genetic relationships between cohorts at these sites were determined. I found high similarity in recovered sequences within and between all cohorts, with cohorts sharing 100% sequence identity across some samples. Phylogenetic reconstruction of the combined datasets indicate panmixia, with samples of all origins belonging to shared genetic lineages. Additional clustering algorithms supported this pattern. The findings of this study indicate that there is strong genetic similarity between both infectious strains and nasal carriage strains and between isolates from all cohorts. This research has implications for healthcare, as it demonstrates that S. aureus from differing environments are genetically similar (often identical), cautioning against delineating strains into nasal carriage or infectious based on origin. This research also informs the study of S. aureus evolution (-) strengthening the conclusion that differentiation at stably selected markers in lineages within differing 'healthcare habitats' is insufficient to explain observed phenotypic differences, and alternative explanations must be explored.
Show less - Date Issued
- 2016
- Identifier
- CFE0006534, ucf:51369
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006534
- Title
- The paths less traveled: Movement of Gopher Tortoises (Gopherus polyphemus) along roads and railways.
- Creator
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Rautsaw, Rhett, Parkinson, Christopher, Mansfield, Kate, Seigel, Richard, University of Central Florida
- Abstract / Description
-
Urbanization and an expanding human population have led to a large degree of habitat destruction and fragmentation. These, in turn, reduce biodiversity and wildlife population sizes on a global scale. Transportation infrastructure, such as roads and railways, are some of the largest contributors to habitat fragmentation. Roads are well-established to negatively impact wildlife, but some studies suggest a potential use in habitat connectivity by functioning as wildlife corridors to connect...
Show moreUrbanization and an expanding human population have led to a large degree of habitat destruction and fragmentation. These, in turn, reduce biodiversity and wildlife population sizes on a global scale. Transportation infrastructure, such as roads and railways, are some of the largest contributors to habitat fragmentation. Roads are well-established to negatively impact wildlife, but some studies suggest a potential use in habitat connectivity by functioning as wildlife corridors to connect distant populations. Railways are similarly known to impact wildlife by increasing mortality rates as well as provide unique risks such as electrocution and entrapment when compared to roads. However, the influence of railways on the movement and behavior of most taxa remains understudied. Here, I used Gopher Tortoises (Gopherus polyphemus) at the John F. Kennedy Space Center as a model system to (1) determine whether roadsides are or could be used as a wildlife corridor to connect distant habitats and (2) evaluate the impacts of railways on tortoise movement and behavior while providing management implications for both roads and railways.To examine the use of roadsides as wildlife corridors, I tracked the movement of individuals found along roadsides using radio-telemetry to determine if tortoises used the roadsides to move between inland and coastal habitat. In addition, I compared home range sizes of tortoises along roads to those of inland and coastal habitats to examine differences in spatial use patterns with regards to roads. I translocated tortoises from distant habitats into the roadside corridors to determine whether they would use the roadsides as a connective route to return to their original capture location. Overall, I determined that roadsides do not function as movement pathways, as even translocated tortoises remained along roads throughout the duration of the study. Instead, roads appear to function as long-term residential areas and potentially suitable habitat. I suggest management of roadsides to reduce mortality and further studies to examine the potential of roadsides acting as ecological traps.To study the impact of railways on tortoise movement and behavior I first used radio-telemetry to track the movement of tortoises found less than 100 m from railways. I simulated movement by using 1000 correlated random walks per tortoise to determine if the number of observed crossing events were significantly less than what would be expected by chance. Second, I measured behavior via continuous focal sampling for one hour to determine railway crossing ability and test for behavioral differences associated with the familiarity of the railways using a principal component analysis. Lastly, I tested if trenches dug underneath the rails could be used as a management strategy to alleviate the impact of railways on tortoises. I found that tortoises are unlikely to cross the railways and the number of observed crossing events were significantly less than what we would expect by chance. Additionally, familiarity with the railway did not have any influence on a tortoise's ability to cross nor their behavior. Trenches were frequently used to move from one side of the railway to the other and are, therefore, a valid management strategy to alleviate the impacts railways have on tortoise mortality, movement, and behavior.Overall, I conclude that transportation infrastructure and the expanding human population have immense impacts on wildlife, especially on turtles and tortoises. I recommend further research continue to identify unique management strategies as well as alternative barriers that may play a large role in a species' decline.
Show less - Date Issued
- 2017
- Identifier
- CFE0006954, ucf:51660
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006954
- Title
- Biogeography and systematics of the Nerodia clarkii/Nerodia fasciata clade in Florida.
- Creator
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Territo, Gregory, Parkinson, Christopher, Hoffman, Eric, Fauth, John, University of Central Florida
- Abstract / Description
-
Biogeography provides a window into the evolutionary history of populations, and helps explain the diversity and distribution of life through time. Viewed from a systematic perspective, biogeographic studies generate convincing arguments to explain the relationships among organisms and categorize them into useful taxonomies. When taxonomies do not reflect evolutionary histories, inaccurate representations of biodiversity confound future studies and conservation efforts. Two thamnophiine...
Show moreBiogeography provides a window into the evolutionary history of populations, and helps explain the diversity and distribution of life through time. Viewed from a systematic perspective, biogeographic studies generate convincing arguments to explain the relationships among organisms and categorize them into useful taxonomies. When taxonomies do not reflect evolutionary histories, inaccurate representations of biodiversity confound future studies and conservation efforts. Two thamnophiine snakes, Nerodia clarkii and Nerodia fasciata, harbor unique morphological and ecological adaptations that obscured natural groupings, leading to controversial taxonomic delimitations. Additionally, population declines documented in N. clarkii compressicauda and N. clarkii taeniata led managers to list N. clarkii taeniata as threatened in 1977. I generated a baseline for continued biogeographic and systematic study of the Nerodia clarkii/fasciata clade. I used mitochondrial DNA to build a parsimony-based haplotype network, infer the phylogenetic relationships between the two species and their thamnophiine relatives, and estimate the divergence times of major N. clarkii/fasciata clades. With these data, I tested biogeographic and systematic hypotheses about the origin and distribution of diversity in this clade. I used principal components analyses to summarize morphological data and discuss ecological observations in search of characters that may unite genetic or taxonomic units. The analyses revealed a peninsular and a panhandle clade in Florida that appeared to diverge as a result of Pleistocene glacial fluctuations. I found no support genetically, morphologically, or ecologically for the current taxonomy, indicating a need for range-wide research to generate revised nomenclature. My results do not support the protection status of N. clarkii taeniata.
Show less - Date Issued
- 2013
- Identifier
- CFE0004760, ucf:49764
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004760
- Title
- Host and Bacterial Determinants of Staphylococcus aureus Nasal Colonization in Humans.
- Creator
-
Muthukrishnan, Gowrishankar, Cole, Alexander, Moore, Sean, Self, William, Parkinson, Christopher, University of Central Florida
- Abstract / Description
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Staphylococcus aureus (SA), an opportunistic pathogen colonizing the anterior nares in approximately 30% of the human population, causes severe hospital-associated and community-acquired infections. SA nasal carriage plays a critical role in the pathogenesis of staphylococcal infections and SA eradication from the nares has proven to be effective in reducing endogenous infections. To understand SA nasal colonization and its relation with consequent disease, assessment of nasal carriage...
Show moreStaphylococcus aureus (SA), an opportunistic pathogen colonizing the anterior nares in approximately 30% of the human population, causes severe hospital-associated and community-acquired infections. SA nasal carriage plays a critical role in the pathogenesis of staphylococcal infections and SA eradication from the nares has proven to be effective in reducing endogenous infections. To understand SA nasal colonization and its relation with consequent disease, assessment of nasal carriage dynamics among a diverse population and determining factors responsible for SA nasal carriage have become major imperatives.Here, we report on an extensive longitudinal monitoring of SA nasal carriage in 109 healthy individuals over a period of up to three years to assess nasal carriage dynamics. Phylogenetic analyses of SA housekeeping genes and hypervariable virulence genes revealed that not only were SA strains colonizing intermittent and persistent nasal carriers genetically similar, but no preferential colonization of specific SA strains in these carriers was observed over time. These results indicated that other non-SA factors could be involved in determining specific carriage states. Therefore, to elucidate host responses during SA nasal carriage, we performed human SA nasal recolonization in a subset of SA nasal carriers within our cohort. In these studies, SA colonization levels were determined, and nasal secretions were collected and analyzed for host immune factors responsible for SA nasal carriage. Interestingly, we observed that stimulation of host immune responses lead to clearance of SA while sustained SA colonization was observed in hosts that did not mount a response during carriage. Further, analysis of nasal secretions from hosts revealed that proinflammatory cytokines and chemokines were significantly induced during SA nasal clearance suggesting that innate immune effectors influence carriage.SA utilizes a repertoire of surface and secreted proteins to evade host immune response and successfully colonize the nose. Analysis of the most abundant immunoevasive proteins in the exoproteome of SA nasal carrier strains revealed that expression levels of Staphylococcal protein A (SPA) produced by SA nasal carrier strains in vitro corresponded to the level of persistence of SA in the human nose. To determine if SPA is involved in modulating the host's response to SA colonization, a subset of participants in our cohort was nasally recolonized with equal concentrations of both wild-type (WT) and spa-disrupted (?spa) autologous strains of SA. Interestingly, ?spa strains were eliminated from the nares significantly faster than WT when the host mounted an immune response, suggesting that the immunoevasive role of SPA is a determinant of carriage persistence. Collectively, this report augments our understanding of SA nasal carriage dynamics, in addition to identifying important host and microbial determinants that influence SA nasal colonization in humans. Better understanding of this phenomenon can lead to improved preventative strategies to thwart carriage-associated SA infections.
Show less - Date Issued
- 2014
- Identifier
- CFE0005673, ucf:50173
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005673
- Title
- Antimicrobial Peptide Resistance and Immunomodulation by HIV-1 gp41.
- Creator
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Wood, Matthew, Cole, Alexander, Chai, Karl, Teter, Kenneth, Parkinson, Christopher, University of Central Florida
- Abstract / Description
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Fusion inhibitors are a class of antiretroviral drugs used to prevent entry of HIV into host cells. Many of the fusion inhibitors being developed, including the drug enfuvirtide (ENF), are peptides designed to mimic, and thereby competitively inhibit, the viral fusion protein gp41. An exception to this is a class of cyclic, cationic, antimicrobial peptides known as ?-defensins, which are produced by many non-human primates and exhibit broad-spectrum antiviral and antibacterial activity....
Show moreFusion inhibitors are a class of antiretroviral drugs used to prevent entry of HIV into host cells. Many of the fusion inhibitors being developed, including the drug enfuvirtide (ENF), are peptides designed to mimic, and thereby competitively inhibit, the viral fusion protein gp41. An exception to this is a class of cyclic, cationic, antimicrobial peptides known as ?-defensins, which are produced by many non-human primates and exhibit broad-spectrum antiviral and antibacterial activity. Currently, the ?-defensin analog RC-101 is being developed as a microbicide to prevent sexual transmission of HIV-1. Understanding potential RC-101 resistance, and how resistance to other fusion inhibitors affects RC-101 susceptibility, is critical for future development.Partial drug resistance due to genetic variability within HIV-1 presents a major hurdle in microbicide development. Drug-resistance mutations, whether naturally occurring or resulting from selection during treatment, often apply to many drugs in a particular class. Combining different drug classes into a single microbicide should provide greater protection against the growing variability observed in HIV. Our work has identified the beneficial effects of combining the fusion inhibitor RC-101 and the RT inhibitor CSIC to prevent transmission of clinically isolated and drug-resistant HIV-1.Several aspects of HIV-1 virulence and pathogenesis are mediated by the envelope protein gp41. Additionally, peptides derived from the gp41 ectodomain have been shown to induce chemotaxis in monocytes and neutrophils. While this chemotactic activity has been characterized, it is not known how these peptides could be produced under biological conditions. Our findings demonstrate that the epithelial serine protease matriptase efficiently cleaves the gp41 HR1 region at conserved residues into a chemotactic peptide.Here, we present evidence that advances our understanding of resistance to peptide entry inhibitors, reveals a potential benefit to combining specific drugs in an antiviral microbicide, and identifies a pathway by which HIV-1 may generate peptides to exploit host immunity. This work thereby facilitates improved methods in countering drug resistance and the development of new antiviral approaches to prevent HIV-1 transmission. Additionally, we have revealed basic mechanistic evidence that shed light on our current understanding of HIV-1 infection. Specifically, our focus on gp41 provides much needed insight into its role in membrane fusion, drug susceptibility, and modification of host responses.
Show less - Date Issued
- 2014
- Identifier
- CFE0005560, ucf:50286
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005560
- Title
- Evolution and distribution of phenotypic diversity in the venom of Mojave Rattlesnakes (Crotalus scutulatus).
- Creator
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Strickland, Jason, Savage, Anna, Parkinson, Christopher, Hoffman, Eric, Rokyta, Darin, University of Central Florida
- Abstract / Description
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Intraspecific phenotype diversity allows for local adaption and the ability for species to respond to changing environmental conditions, enhancing survivability. Phenotypic variation could be stochastic, genetically based, and/or the result of different environmental conditions. Mojave Rattlesnakes, Crotalus scutulatus, are known to have high intraspecific venom variation, but the geographic extent of the variation and factors influencing venom evolution are poorly understood. Three primary...
Show moreIntraspecific phenotype diversity allows for local adaption and the ability for species to respond to changing environmental conditions, enhancing survivability. Phenotypic variation could be stochastic, genetically based, and/or the result of different environmental conditions. Mojave Rattlesnakes, Crotalus scutulatus, are known to have high intraspecific venom variation, but the geographic extent of the variation and factors influencing venom evolution are poorly understood. Three primary venom types have been described in this species based on the presence (Type A) or absence (Type B) of a neurotoxic phospholipase A2 called Mojave toxin and an inverse relationship with the presence of snake venom metalloproteinases (SVMPs). Individuals that contain both Mojave toxin and SVMPs, although rare, are the third, and designated Type A + B. I sought to describe the proteomic and transcriptomic venom diversity of C. scutulatus across its range and test whether diversity was correlated with genetic or environmental differences. This study includes the highest geographic sampling of Mojave Rattlesnakes and includes the most venom-gland transcriptomes known for one species. Of the four mitochondrial lineages known, only one was monophyletic for venom type. Environmental variables poorly correlated with the phenotypes. Variability in toxin and toxin family composition of venom transcriptomes was largely due to differences in transcript expression. Four of 19 toxin families identified in C. scutulatus account for the majority of differences in toxin number and expression variation. I was able to determine that the toxins primarily responsible for venom types are inherited in a Mendelian fashion and that toxin expression is additive when comparing heterozygotes and homozygotes. Using the genetics to define venom type is more informative and the Type A + B phenotype is not unique, but rather heterozygous for the PLA2 and/or SVMP alleles. Intraspecific venom variation in C. scutulatus highlights the need for fine scale ecological and natural history information to understand how phenotypic diversity is generated and maintained geographically through time.
Show less - Date Issued
- 2018
- Identifier
- CFE0007252, ucf:52198
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007252
- Title
- Evolutionary Relationships Among Staphylococci and the Prevention of Staphylococcus aureus Nasal Colonization.
- Creator
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Lamers, Ryan, Cole, Alexander, Parkinson, Christopher, Chai, Xinqing, Moore, Sean, University of Central Florida
- Abstract / Description
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Staphylococcus is a significant cause of human infection and mortality, worldwide. Currently, there are greater than 60 taxa within Staphylococcus, and nearly all are pathogenic. The collective potential for virulence among species of Staphylococcus heightens the overall clinical significance of this genus and argues for a thorough understanding of the evolutionary relationships among species. Within Staphylococcus, aureus is the most common cause of human infection, where nasal carriage of...
Show moreStaphylococcus is a significant cause of human infection and mortality, worldwide. Currently, there are greater than 60 taxa within Staphylococcus, and nearly all are pathogenic. The collective potential for virulence among species of Staphylococcus heightens the overall clinical significance of this genus and argues for a thorough understanding of the evolutionary relationships among species. Within Staphylococcus, aureus is the most common cause of human infection, where nasal carriage of this bacterium is a known risk factor for autoinfection. The predisposition to infection by nasal carriers of S. aureus, and the ease with which strains are transferred between individuals, suggests that nasal carriage is a major vector for the transmission of virulent strains throughout the community. This hypothesis, however, has not been assessed in any great detail to identify the genetic relationships between clinical isolates of S. aureus and those strains being carried asymptomatically throughout the community. Also lacking within this field is a unified and robust estimate of phylogeny among species of Staphylococcus.Here, we report on a highly unified species phylogeny for Staphylococcus that has been derived using multilocus nucleotide data under multiple Bayesian and maximum likelihood approaches. Our findings are in general agreement with previous reports of the staphylococcal phylogeny, although we identify multiple previously unreported relationships. Regardless of methodology, strong nodal support and high topological agreement was observed with only minor variations in results between methods. Based on our phylogenetic estimates, we propose that Staphylococcus species can be evolutionarily clustered into 15 groups, and six species groups. In addition, our more defined phylogenetic analyses of S. aureus revealed strong genetic associations between both nasal carriage strains and clinical isolates. Genetic analyses of hypervariable regions from virulence genes revealed that not only do clinically relevant strains belong to identical genetic lineages as the nasal carriage isolates, but they also exhibited 100% sequence similarity within these regions. Our findings indicate that strains of S. aureus being carried asymptomatically throughout the community via nasal colonization are genetically related to those responsible for high levels of infection and mortality.Due to nasal carriage of S. aureus being a risk factor for autoinfection, standardized preoperative decolonization has become a major consideration for the prevention of nosocomial infection. Toward this end, we have identified the macrocyclic ?-defensin analogue RC-101 as a promising anti-S. aureus agent for nasal decolonization. RC-101 exhibited bactericidal effects against S. aureus in both epithelium-free systems, and ex vivo models containing human airway epithelia. Importantly, RC-101 exhibited potent anti-S. aureus activities against all strains tested, including USA300. Moreover, RC-101 significantly reduced the adherence, survival, and proliferation of S. aureus on human airway epithelia without any noted cellular toxicity or the induction of a proinflammatory response. Collectively, our findings identify RC-101 as a potential preventative of S. aureus nasal colonization.
Show less - Date Issued
- 2011
- Identifier
- CFE0004124, ucf:49092
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004124
- Title
- Conservation and population biology: genetics, demography and habitat requirements of the Atlantic coast beach mice.
- Creator
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Kalkvik, Haakon, Parkinson, Christopher, Stout, I, Hoffman, Eric, Weishampel, John, Doonan, Terry, University of Central Florida
- Abstract / Description
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The conservation biology field seeks to preserve biodiversity and the processes shaping that variation. Conservation biology is intimately tied to evolutionary research, in order to identify evolutionary distinct lineages that may be in danger of disappearing. Interestingly, patterns and processes of lineage divergence and persistence change with respect to spatial and temporal scale. I seek to evaluate biodiversity, the factors that have shaped this heterogeneity, and how this variability...
Show moreThe conservation biology field seeks to preserve biodiversity and the processes shaping that variation. Conservation biology is intimately tied to evolutionary research, in order to identify evolutionary distinct lineages that may be in danger of disappearing. Interestingly, patterns and processes of lineage divergence and persistence change with respect to spatial and temporal scale. I seek to evaluate biodiversity, the factors that have shaped this heterogeneity, and how this variability persists. To accomplish this I used a phylogeographic approach as well as niche and population modeling on the Peromyscus maniculatus species group found widely distributed in North America. My emphasis was on the southeastern U.S. species P. polionotus and its distinct beach forms. At a continental scale, I found that environmental niches are likely involved in generating and/or maintaining genetic lineages within the P. maniculatus species group. These findings add to a growing number of studies that have identified lineages occupying different environmental spaces. At a regional scale, I supported the hypothesis that barrier islands on the Atlantic coast of Florida were colonized by an ancestral form of P. polionotus by a single colonization, from the central Florida area. Subsequently, at least two distinct lineages diverged (P. p. phasma and P. p. niveiventris). I also found evidence that suggests that the extinct form of beach mouse (P. p. decoloratus) is part of the P. p. phasma lineage. At the population level, I evaluated changes in genetic diversity in historical samples compared to those that experienced recent human encroachment on natural habitat I used tissue preserved in natural history collections to compare with live-trapped specimens, and found that P. p. niveiventris has maintained historical genetic diversity levels. I suggest that the continuation of historical levels of genetic diversity is due to the presence of a single large area of continuous habitat in the central portion of the species' current distribution. Finally, I evaluated the importance of scrub and beach habitat to the population dynamics of beach mice. Beach mice have traditionally have been associated with beach dunes rather than with the scrub habitat found more inland on barrier islands. Using almost three years of capture-recapture data from Cape Canaveral Air Force Station (CCAFS), I created a stochastic matrix model to assess the relative contribution of populations from the two different habitats to a variety of demographic measures. Both field data and model results provided evidence that the population dynamics of beach mice may rely much more on scrub habitat than formerly documented. Overall, my research emphasized a hierarchical approach to evaluate biodiversity and the processes shaping differentiation at different spatial and temporal scales. The methods and findings give insight into speciation at different scales, and can be applied to a wide range of taxa for questions related to evolutionary and conservation biology.
Show less - Date Issued
- 2012
- Identifier
- CFE0004392, ucf:49372
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004392
- Title
- Phylogenetic Community Structure of Aquatic Beetle Assemblages in a Multi-Wetland Experiment.
- Creator
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Kelly, Sandor, Jenkins, David, Parkinson, Christopher, Crampton, William, Song, Hojun, University of Central Florida
- Abstract / Description
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Phylogenetic Community Structure (PCS) metrics are becoming more common in community ecology. PCS metrics estimate the phylogenetic relatedness among members of an ecological community or assemblage. If ecological traits are conserved, then phylogenetic clustering (i.e., taxa are more closely related than expected by chance) indicates habitat filtering as the key process in community assembly. On the other hand, a pattern of phylogenetic overdispersion (i.e., taxa are more distantly related...
Show morePhylogenetic Community Structure (PCS) metrics are becoming more common in community ecology. PCS metrics estimate the phylogenetic relatedness among members of an ecological community or assemblage. If ecological traits are conserved, then phylogenetic clustering (i.e., taxa are more closely related than expected by chance) indicates habitat filtering as the key process in community assembly. On the other hand, a pattern of phylogenetic overdispersion (i.e., taxa are more distantly related than expected by chance) suggests competition is dominant. Most studies to date have used PCS of unmanipulated ecosystems, but the value of PCS metrics will be best revealed in experiments. This project used PCS for aquatic beetle (Coleoptera) assemblages in experimentally manipulated seasonal wetlands on a cattle ranch in south-central Florida, and compared PCS metrics to standard ecological metrics. Wetlands were experimentally treated with all combinations of pasture management, fencing to exclude cattle, and controlled burning during 2006-2009. Beetle assemblages in fenced wetlands were significantly more overdispersed compared to non-fenced wetlands, suggesting that this treatment decreases habitat filtering, causing competition to become the dominant process in community formation. There was also a significant pasture x fence x burn interaction effect, with assemblages in wetlands differing in PCS depending on what combination of the three treatments were applied. Phylogenetic Diversity (PD (-) a measure of branch length of a community or assemblage on a phylogenetic tree) was highly correlated with genera richness (number of genera), and these metrics along with the expected number of genera (D (-) an ecological diversity index) found significant differences among burn treatments and a pasture x burn interaction. The results of this study indicate that PCS metrics complement classical ecological methods and should be widely applied.
Show less - Date Issued
- 2012
- Identifier
- CFE0004394, ucf:49388
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004394
- Title
- Using Molecular Genetic and Demographic Tools to Improve Management of Ex Situ Avian Populations.
- Creator
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Ferrie, Gina, Hoffman, Eric, Parkinson, Christopher, Quintana-Ascencio, Pedro, Bettinger, Tamara, University of Central Florida
- Abstract / Description
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Small populations, specifically those that are isolated from others, are more prone to extinction than larger inter-connected populations. The risks that these small isolated populations face include loss of genetic diversity due to founder effects and inbreeding due to population bottlenecks, as well as demographic uncertainty due to fluctuating fecundity and mortality rates and impacts of external environmental factors. Ex situ populations, including those managed as conservation breeding...
Show moreSmall populations, specifically those that are isolated from others, are more prone to extinction than larger inter-connected populations. The risks that these small isolated populations face include loss of genetic diversity due to founder effects and inbreeding due to population bottlenecks, as well as demographic uncertainty due to fluctuating fecundity and mortality rates and impacts of external environmental factors. Ex situ populations, including those managed as conservation breeding programs with species recovery aims, as well as those that do not have reintroduction goals but are managed for long term population sustainability, suffer from the same extinction risks as small and isolated natural populations. Using three separate avian species which have different life histories and population structures, I investigated impacts of multiple genetic and demographic management strategies on these ex situ populations. I examined the use of molecular genetic datasets including microsatellites and single nucleotide polymorphisms (SNPs) to determine their utility for reconstructing pedigrees, examining individual relatedness within populations, and compared results of measuring genetic diversity through theoretical methods verses those obtained from a molecular dataset. These methods can then ultimately be applied to improve future management including improving studbook datasets and to measure actual loss of genetic diversity. I also used analytical strategies including population viability analysis to determine how management practices influence demographic parameters and determine the future probability of population extinction. The genetic and demographic analyses of both the historic management of an ex situ population, and its current status, are a first step in hypothesizing the potential directions for future management and understanding the likelihood of survival of an ex situ population.
Show less - Date Issued
- 2017
- Identifier
- CFE0006940, ucf:51670
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006940
