Current Search: Savage, Anna (x)
View All Items
(1 - 10 of 10)
- Title
- INFECTION DYNAMICS OF HERPESVIRUS IN GOPHER TORTOISES.
- Creator
-
Saldanha, Joanne, Savage, Anna, University of Central Florida
- Abstract / Description
-
Gopherus polyphemus, commonly known as the Gopher Tortoise, is a dryland reptile native to the southeastern United States. It is commonly a resident of longleaf pine and dry oak sand hill habitats. It is considered a keystone species because they dig deep burrows that provide shelter to them as well as many other animals. Habitat loss, fragmentation, and disease are major threats and have caused this species to be federally listed as a threatened species under the Endangered Species Act (ESA)...
Show moreGopherus polyphemus, commonly known as the Gopher Tortoise, is a dryland reptile native to the southeastern United States. It is commonly a resident of longleaf pine and dry oak sand hill habitats. It is considered a keystone species because they dig deep burrows that provide shelter to them as well as many other animals. Habitat loss, fragmentation, and disease are major threats and have caused this species to be federally listed as a threatened species under the Endangered Species Act (ESA). Disease is a major threat to the gopher tortoise's survival, and with declining populations, the need to investigate pathogens is crucial. Herpesvirus, is known to contribute to upper respiratory tract diseases (URTD) in G. polyphemus and is the primary focus of this project. Due to high mutation rates in the virus, a modified version of PCR, nested PCR, was conducted on eye and nose swabs and blood samples obtained from G. polyphemus to detect the presence of the alpha herpesvirus pathogen. The positive samples were then sent for genetic sequencing to confirm the occurrence of the pathogen. The detectability of Herpesvirus in eye and nose swabs was compared to blood and lymph samples and statistical tests concluded that both sample types had the same detectability.
Show less - Date Issued
- 2018
- Identifier
- CFH2000376, ucf:45786
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFH2000376
- Title
- AEROMONAS HYDROPHILA IN AMPHIBIANS: HARMLESS BYSTANDER OR OPPORTUNISTIC PATHOGEN.
- Creator
-
Rivas, Zachary P, Savage, Anna Evangeline, University of Central Florida
- Abstract / Description
-
For several decades amphibian populations have been declining. Historically, the bacterium A. hydrophila (Ah) was hypothesized to be the causal factor in amphibian disease and population declines. However, with the discovery of a chytrid fungus, Batrachochytrium dendrobatidis (Bd) in 1998, which was identified on the skin of amphibians during documented mortality events, Ah research became of minor interest as focus shifted to Bd. Recent studies into the immunocompromising abilities of Bd,...
Show moreFor several decades amphibian populations have been declining. Historically, the bacterium A. hydrophila (Ah) was hypothesized to be the causal factor in amphibian disease and population declines. However, with the discovery of a chytrid fungus, Batrachochytrium dendrobatidis (Bd) in 1998, which was identified on the skin of amphibians during documented mortality events, Ah research became of minor interest as focus shifted to Bd. Recent studies into the immunocompromising abilities of Bd, however, have opened new questions about its relationship with Ah and their combined effects on a host. In this study, I explore the relationship between infection with these two pathogens, Bd and Ah, in two amphibian species from distinct regions of the United States. I developed a novel qPCR assay to measure the microbial load of Ah on the skin of two anuran species, Lithobates yavapaiensis (N=232) and Pseudacris ornata (N=169), which have confirmed Bd infections. I use a logistic regression model to identify whether significant relationships exist between these two pathogens, disease, and death. I find that even amongst the most severely infected frogs, Ah is not detectable on the skin and only appears post-mortem. I therefore conclude that Ah is an opportunistic bacterial pathogen, scavenging on anurans only after mortality events. This research is the first known study to quantitatively assess Ah in amphibians in conjunction with Bd. While there is no causal relationship between these pathogens, future work will examine potential Ah infections in other organs to more fully understand the relationship between Bd and Ah.
Show less - Date Issued
- 2016
- Identifier
- CFH2000013, ucf:45589
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFH2000013
- Title
- Characterizing biogeochemical shifts in two Salix Caroliniana Michx. encroached freshwater subtropical marshes.
- Creator
-
Ho, Janet, Chambers, Lisa, Hinkle, Ross, Savage, Anna, University of Central Florida
- Abstract / Description
-
Shrub encroachment is a common disturbance in wetlands, but little is known about how shrub encroachment impacts functions such as carbon (C) storage and nitrogen (N) cycling. The objective of this thesis was to identify differences in physiochemical properties (within soil, water and leaf tissue) and biogeochemical processes (soil respiration, enzyme activity, litter decomposition, and N cycling) in two subtropical freshwater marshes encroached by coastal plain willow (Salix caroliniana...
Show moreShrub encroachment is a common disturbance in wetlands, but little is known about how shrub encroachment impacts functions such as carbon (C) storage and nitrogen (N) cycling. The objective of this thesis was to identify differences in physiochemical properties (within soil, water and leaf tissue) and biogeochemical processes (soil respiration, enzyme activity, litter decomposition, and N cycling) in two subtropical freshwater marshes encroached by coastal plain willow (Salix caroliniana Michx.). Two study regions (Moccasin Island and Lake Apopka) were selected because of their location in the St. John's River watershed and their unique histories and hydroperiod, allowing for an investigation of how synonymous the effects of willow-encroachment are across sites. A stratified random sampling design was employed in each region, identifying three plot types: willow ((>)80 % willow aboveground coverage), adjacent marsh ((>)80% herbaceous aboveground coverage and (<)1 m from willows), and control marsh ((>)80% herbaceous aboveground coverage and (>)10 m from willows) plots. Triplicate soil samples were collected in each plot in the wet and dry seasons of 2017 and analyzed for physiochemical properties (bulk density, moisture, nutrient content) and used in laboratory assays to measure soil respiration, enzyme activity, and potential N mineralization and denitrification rates. Leaf tissue was collected from the dominant vegetation in each plot and analyzed for nutrient content (total C, lignin-C, and total N). Short-term litter decay rate was determined using a litter-bag field experiment. Bioavailable N and dissolved organic C (DOC) concentrations were determined from surface and porewater collected from the center of each plot. In Moccasin Island, lower decomposition rates and greater denitrification, potential N mineralization, and soil C and N content were detected in willow and adjacent marsh plots, suggesting greater C storage and N cycling in willow-encroached marshes compared to non-encroached control marshes in Moccasin Island. Conversely, soil C and N content was lowest in willow plots in Lake Apopka. Decomposition and microbial activity (enzyme activity and respiration) were lowest in willow dominated areas and correlated to soil nutrient concentrations. In both regions, microbial compositional changes (gene copy number) were detected between plot types, mainly in bacteria (?-proteobacteria and Bacteroidetes) for Moccasin Island and archaea and fungi abundance in Lake Apopka. Ultimately, willow plots in both regions had greater lignin-C content and short-term litter C storage. Greater bioavailable N was also observed in adjacent and/or willow plots in both regions. However, soil C storage and N cycling differences were not synonymous between the two regions. Future studies of willow effects will need to look at multiple sites or risk making inaccurate generalizations. From the findings from this study, wetland processes can be altered in willow-encroached marshes and this data can help land managers decide where to allocate resources based on valued ecosystem services.
Show less - Date Issued
- 2018
- Identifier
- CFE0007015, ucf:52043
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007015
- Title
- The Evolution of Peristenus (Hymenoptera: Braconidae): Taxonomy, Phylogenetics and Ecological Speciation.
- Creator
-
Zhang, Yuanmeng, Sharanowski, Barbara, Hoffman, Eric, Savage, Anna, Marcus, Jeffrey, University of Central Florida
- Abstract / Description
-
Parasitoid wasps are ecologically and economically important as biological control agents. However, little is known about the diversity, distribution and biology of most hymenopteran parasitoids due to their small size, morphological conservatism, and complex life styles. The focus of my PhD research was to investigate the evolution and speciation of euphorine braconid wasps, using a combination of multilocus phylogenetics and population genomic techniques combined with traditional taxonomy....
Show moreParasitoid wasps are ecologically and economically important as biological control agents. However, little is known about the diversity, distribution and biology of most hymenopteran parasitoids due to their small size, morphological conservatism, and complex life styles. The focus of my PhD research was to investigate the evolution and speciation of euphorine braconid wasps, using a combination of multilocus phylogenetics and population genomic techniques combined with traditional taxonomy. The three data chapters of my dissertation are divided into different taxonomic ranks of euphorine braconids, focusing on genera, species, and populations. For chapter 2, I built a multilocus phylogeny of the tribe Euphorini with extensive taxa sampling around the globe. I confirmed the monophyly of Peristenus and Leiophron, two important biological control agents, and provided updated generic concepts and identification resources to aid applied researchers. In Chapters 3 and 4, I focused on cryptic species within the Peristenus pallipes complex in North America. I used an integrative taxonomic approach to resolve the taxonomic confusion within the Nearctic Peristenus pallipes complex (Chapter 3), then I used ddRADSeq to examine their evolutionary relationships with their Lygus hosts (Chapter 4). My dissertation provided a comprehensive analysis of Peristenus at multiple taxonomic ranks using phylogenetics and population genomics, providing insights into their evolutionary history that can be extrapolated into other groups of parasitoid wasps. The results from these studies also advanced our understanding of this group of animals of theoretical, economical, and conservation importance.
Show less - Date Issued
- 2018
- Identifier
- CFE0007272, ucf:52194
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007272
- Title
- Unearthing the past and present of a semi-fossorial lizard: conservation genetics, phylogeography, and taxonomy of Plestiodon egregius.
- Creator
-
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
- Assessment of Staphylococcus aureus Genetics: Clinical versus Community Epidemiology.
- Creator
-
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 Effect of Parental Population Density on Offspring Immune Function.
- Creator
-
Davis, Dana, Fedorka, Kenneth, Savage, Anna, Hoffman, Eric, University of Central Florida
- Abstract / Description
-
It is well known that an individual's environment, genetic code, and gene by environment interactions have an effect on its overall phenotype. However, there is a growing body of work that shows that parents can have an effect on their offspring's phenotype beyond the inherited genetic code. Studies have shown that parents may affect their offspring through physiological mechanisms such as egg provisioning and epigenetic effects and through behavioral mechanisms such as maternal care. In many...
Show moreIt is well known that an individual's environment, genetic code, and gene by environment interactions have an effect on its overall phenotype. However, there is a growing body of work that shows that parents can have an effect on their offspring's phenotype beyond the inherited genetic code. Studies have shown that parents may affect their offspring through physiological mechanisms such as egg provisioning and epigenetic effects and through behavioral mechanisms such as maternal care. In many of these cases, the parental effect is triggered by an environmental cue. Previous work has shown that density can impact immune function and cuticle color in insects - two phenotypic traits that are pleiotropically linked. Additional work has shown that parental density can have impacts on offspring immune function, as well. However, previous studies utilized insect species that show a strict density dimorphic phenotype where individuals reared at high densities exhibit increased immune function and much darker cuticles than their low density counterparts, which is not an accurate representation of most insect systems as most insect systems show a more continuous response to density effects. Also, previous work has not determined the parental origin of density effects on offspring immune function and cuticle color. It has been suggested that parental density effects may be due to maternal egg provisioning and that paternal effects may be minimal. However, knowledge of parental origin would give us a better insight into the possible mechanisms of these density driven parental effects and provide a direction for future research. In my study, we used Drosophila melanogaster in order to determine (1) if density affects immune function and cuticle color in a species that shows a continuous response to density, (2) if parental density affects offspring immune function and cuticle color, and (3) if the source of these parental effects are of a maternal origin only or if these effects are of a paternal origin, as well. We found that there is an effect of density on immune function and cuticle color in the parents in a more common insect system and parental density had an effect on offspring phenotype, as well. Most notably, we found that, in addition to the effects of maternal density, these parental effects on offspring phenotype were a response to paternal density, as well.
Show less - Date Issued
- 2017
- Identifier
- CFE0006580, ucf:51355
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006580
- Title
- Evolution and distribution of phenotypic diversity in the venom of Mojave Rattlesnakes (Crotalus scutulatus).
- Creator
-
Strickland, Jason, Savage, Anna, Parkinson, Christopher, Hoffman, Eric, Rokyta, Darin, University of Central Florida
- Abstract / Description
-
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
- Behavioral and disease ecology of Gopher Tortoises (Gopherus polyphemus) post exclusion and relocation with a novel approach to homing determination.
- Creator
-
Napier, Johnathan, Savage, Anna, Moore, Sean, Vonkalm, Laurence, Fedorka, Kenneth, University of Central Florida
- Abstract / Description
-
In the wake of human expansion, relocations and the loss of habitat can be stressful to an organism, plausibly leading to population declines. The gopher tortoise (Gopherus polyphemus) is a keystone species that constructs burrows it shares with 362 commensal species. Frequent exclusions and relocations and long generation times have contributed to G. polyphemus being State-designated as Threatened in Florida. Prior studies have indicated that G. polyphemus may possess homing behavior and...
Show moreIn the wake of human expansion, relocations and the loss of habitat can be stressful to an organism, plausibly leading to population declines. The gopher tortoise (Gopherus polyphemus) is a keystone species that constructs burrows it shares with 362 commensal species. Frequent exclusions and relocations and long generation times have contributed to G. polyphemus being State-designated as Threatened in Florida. Prior studies have indicated that G. polyphemus may possess homing behavior and thus be able to counteract stressors due to relocation and exclusion. I radiotracked a cohort of G. polyphemus for 11 months following excavation, relocation, and exclusion due to a pipeline construction project. In conjunction with analyzing G. polyphemus movement patterns post-release, I developed novel statistical methodologies with broad application for movement analysis and compared them to traditional analyses. I evaluated habitat usage, burrowing behavior, movements, growth, and disease signs among control versus relocated and excluded individuals and among sexes and size classes, forming predictors for behavior and disease risk. I found statistical support that my new methodology is superior to previous statistical tests for movement analyses. I also found that G. polyphemus engages in homing behavior, but only in males. Behavioral differences were also found between the sexes with respect to burrowing behavior. Overall health, disease prevalence, and immune response were unaffected by relocation and exclusion, nor were they statistically correlated. Signs were unreliable as etiological agents, outperformed by serological detection. I determined that the Sabal Trail pipeline as a potential stressor did not affect movement behavior, homing, nor the disease/immune profile of G. polyphemus in this study.
Show less - Date Issued
- 2018
- Identifier
- CFE0007581, ucf:52581
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007581
- Title
- Computational Approaches for Binning Metagenomic Reads.
- Creator
-
Wang, Ying, Hu, Haiyan, Li, Xiaoman, Zhang, Shaojie, Wu, Annie, Savage, Anna, University of Central Florida
- Abstract / Description
-
Metagenomics uses sequencing technologies to study genetic sequences from whole microbial communities. Binning metagenomic reads is the most fundamental step in metagenomic studies, which is essential for the understanding of microbial functions, compositions, and interactions in environmental samples. Various taxonomy-dependent and taxonomy-independent approaches have been developed based on information such as sequence similarity, sequence composition, or k-mer frequency. However, there is...
Show moreMetagenomics uses sequencing technologies to study genetic sequences from whole microbial communities. Binning metagenomic reads is the most fundamental step in metagenomic studies, which is essential for the understanding of microbial functions, compositions, and interactions in environmental samples. Various taxonomy-dependent and taxonomy-independent approaches have been developed based on information such as sequence similarity, sequence composition, or k-mer frequency. However, there is still room for improvement, and it is still challenging to bin reads from species with similar or low abundance or to bin reads from unknown species.In this dissertation, we introduce one taxonomy-independent and three taxonomy-dependent approaches to improve the performance of metagenomic reads binning. The taxonomy-independent method called MBBC, bins reads by considering k-mer frequency in reads without reference genomes. The first two taxonomy-dependent methods both bin reads by measuring the similarity of reads to the trained Markov Chains from different taxa. The major difference between these two methods is that the first one selects the potential taxa with the taxonomical decision tree, while the second one, called MBMC, selects potential taxa using ordinary least squares (OLS) method. The third taxonomy-dependent method bins reads by combining the methods of MBMC with clustering Markov chains from the assembled reads. By testing on both simulated and real datasets, these tools showed superior or comparable performance with various the state of the art methods. We anticipate that our tools can significantly improve the accuracy of metagenomic reads binning and thus be widely applied in real environmental samples.
Show less - Date Issued
- 2016
- Identifier
- CFE0006515, ucf:51380
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006515
