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A Time-Course Analysis of Behavioral Plasticity and Differential Gene Expression Patterns in Response to Density in Schistocerca americana (Orthoptera: Acrididae)
Title
A Time-Course Analysis of Behavioral Plasticity and Differential Gene Expression Patterns in Response to Density in Schistocerca americana (Orthoptera: Acrididae).
Creator
Gotham, Steven, Song, Hojun, Vonkalm, Laurence, Fedorka, Kenneth, University of Central Florida
Abstract / Description
Phenotypic plasticity is the ability of the genotype to express alternative phenotypes in response to different environmental conditions and this is considered to be an adaptation in which a species can survive and persist in a rapidly changing environment. Some grasshoppers and locusts are capable of expressing an extreme form of density-dependent phenotypic plasticity, known as locust phase polyphenism. At low population density, the individuals typically have a cryptic coloration as nymphs...
Show morePhenotypic plasticity is the ability of the genotype to express alternative phenotypes in response to different environmental conditions and this is considered to be an adaptation in which a species can survive and persist in a rapidly changing environment. Some grasshoppers and locusts are capable of expressing an extreme form of density-dependent phenotypic plasticity, known as locust phase polyphenism. At low population density, the individuals typically have a cryptic coloration as nymphs, are less active, and only seek out conspecifics for reproductive purposes. At high density, however, they develop a drastically different phenotype in which they have a conspicuous coloration, are much more active, and tend to stay together in large groups. The American Birdwing grasshopper, Schistocerca americana, is a non-swarming species related to the desert locust, S. gregaria, which shows density-dependent phenotypic plasticity in behavior, color, and morphology. In this thesis, I have identified the duration of crowding necessary for a 6th instar S. americana reared in the isolated condition to express the typical crowded behavior. The behavior changed after just one hour of crowding and the effect of crowding diminished after 48 hours to near-complete isolated behavior. In reverse, the crowded condition was isolated, but behavior did not significantly change over time. Gene expression of the following three genes suspected of having a role in behavior change were investigated based on studies of S. gregaria: protein kinase A (PKA), L-Tryptophan-5-monooxygenase (T-5), and Aromatic L-amino acid decarboxylase (Decarb). T-5 was up-regulated in the long-term isolated condition compared to the long-term crowded condition. T-5 and Decarb were up-regulated in isolated individuals that were crowded for 10 hours compared to the long-term isolated condition. This study represents a novel contribution in the study of phenotypic plasticity as it establishes the time course of behavioral and molecular plasticity in a non-swarming grasshopper for the first time.
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Date Issued
2014
Identifier
CFE0005799, ucf:50049
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0005799
Character Evolution and Microbial Community Structure in a Host-associated Grasshopper
Title
Character Evolution and Microbial Community Structure in a Host-associated Grasshopper.
Creator
Raszick, Tyler, Song, Hojun, Fedorka, Kenneth, Hoffman, Eric, University of Central Florida
Abstract / Description
The spotted bird grasshopper, Schistocerca lineata Scudder (Orthoptera: Acrididae), is a widely distributed species found throughout most of the continental United States and southern Canada. This species is known to be highly variable in morphology, with many distinct ecotypes across its native range. These ecotypes display high levels of association with type-specific host plants. Understanding the evolutionary relationships among different ecotypes is crucial groundwork for studying the...
Show moreThe spotted bird grasshopper, Schistocerca lineata Scudder (Orthoptera: Acrididae), is a widely distributed species found throughout most of the continental United States and southern Canada. This species is known to be highly variable in morphology, with many distinct ecotypes across its native range. These ecotypes display high levels of association with type-specific host plants. Understanding the evolutionary relationships among different ecotypes is crucial groundwork for studying the process of ecological differentiation. I examine four ecotypes from morphological and phylogeographic perspectives, and look for evidence of distinct evolutionary lineages within the species. I also begin to explore the potential role of the microbial community of these grasshoppers in ecological divergence by using 454 pyrosequencing to see if the microbial community structure reflects the ecology of the grasshoppers. I find support for a distinct aposematic lineage when approaching the data from a phylogeographic perspective and also find that this ecotype tends to harbor a unique bacterial community, different from that of a single other ecotype.
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Date Issued
2014
Identifier
CFE0005540, ucf:50316
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0005540
Phylogenetic Community Structure of Aquatic Beetle Assemblages in a Multi-Wetland Experiment
Title
Phylogenetic Community Structure of Aquatic Beetle Assemblages in a Multi-Wetland Experiment.
Creator
Kelly, Sandor, Jenkins, David, Parkinson, Christopher, Crampton, William, Song, Hojun, University of Central Florida
Abstract / Description
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.
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Date Issued
2012
Identifier
CFE0004394, ucf:49388
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0004394
Computational Methods for Comparative Non-coding RNA Analysis: from Secondary Structures to Tertiary Structures
Title
Computational Methods for Comparative Non-coding RNA Analysis: from Secondary Structures to Tertiary Structures.
Creator
Ge, Ping, Zhang, Shaojie, Guha, Ratan, Stanley, Kenneth, Jha, Sumit, Song, Hojun, University of Central Florida
Abstract / Description
Unlike message RNAs (mRNAs) whose information is encoded in the primary sequences, the cellular roles of non-coding RNAs (ncRNAs) originate from the structures. Therefore studying the structural conservation in ncRNAs is important to yield an in-depth understanding of their functionalities. In the past years, many computational methods have been proposed to analyze the common structural patterns in ncRNAs using comparative methods. However, the RNA structural comparison is not a trivial task,...
Show moreUnlike message RNAs (mRNAs) whose information is encoded in the primary sequences, the cellular roles of non-coding RNAs (ncRNAs) originate from the structures. Therefore studying the structural conservation in ncRNAs is important to yield an in-depth understanding of their functionalities. In the past years, many computational methods have been proposed to analyze the common structural patterns in ncRNAs using comparative methods. However, the RNA structural comparison is not a trivial task, and the existing approaches still have numerous issues in efficiency and accuracy. In this dissertation, we will introduce a suite ofnovel computational tools that extend the classic models for ncRNA secondary and tertiary structure comparisons.For RNA secondary structure analysis, we first developed a computational tool, named PhyloRNAalifold, to integrate the phylogenetic information into the consensus structural folding. The underlying idea of this algorithm is that the importance of a co-varying mutation should be determined by its position on the phylogenetic tree. By assigning high scores to the critical covariances, the prediction of RNA secondary structure can be more accurate. Besides structure prediction, we also developed a computational tool, named ProbeAlign, to improvethe efficiency of genome-wide ncRNA screening by using high-throughput RNA structural probing data. It treats the chemical reactivities embedded in the probing information as pairing attributes of the searching targets. This approach can avoid the time-consuming base pair matching in the secondary structure alignment. The application of ProbeAlign to the FragSeq datasets shows its capability of genome-wide ncRNAs analysis.For RNA tertiary structure analysis, we first developed a computational tool, named STAR3D, to find the global conservation in RNA 3D structures. STAR3D aims at finding the consensus of stacks by using 2D topology and 3D geometry together. Then, the loop regions can be ordered and aligned according to their relative positions in the consensus. This stack-guided alignment method adopts the divide-and-conquer strategy into RNA 3D structural alignment, which has improved its efficiency dramatically. Furthermore, we also have clustered all loop regions in non-redundant RNA 3D structures to de novo detect plausible RNA structural motifs. The computational pipeline, named RNAMSC, was extended to handle large-scale PDB datasets, and solid downstream analysis was performed to ensure the clustering results are valid and easily to be applied to further research. The final results contain many interesting variations of known motifs, such as GNAA tetraloop, kink-turn, sarcin-ricin and t-loops. We also discovered novel functional motifs that conserved in a wide range of ncRNAs, including ribosomal RNA, sgRNA, SRP RNA, GlmS riboswitch and twister ribozyme.
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Date Issued
2016
Identifier
CFE0006104, ucf:51212
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0006104