Biology Commons^™

Insights To Protein Pathogenicity From The Lens Of Protein Evolution, Janelle Nunez-Castilla

FIU Electronic Theses and Dissertations

As protein sequences evolve, differences in selective constraints may lead to outcomes ranging from sequence conservation to structural and functional divergence. Evolutionary protein family analysis can illuminate which protein regions are likely to diverge or remain conserved in sequence, structure, and function. Moreover, nonsynonymous mutations in pathogens may result in the emergence of protein regions that affect the behavior of pathogenic proteins within a host and host response. I aimed to gain insight on pathogenic proteins from cancer and viruses using an evolutionary perspective. First, I examined p53, a conformationally flexible, multifunctional protein mutated in ~50% of human cancers. Multifunctional …

The Evolution Of Bioluminescence Across The Shrimp Family Sergestidae: A Genomic Skimming And Phylogenetic Approach, Charles G. Golighty Iii

FIU Electronic Theses and Dissertations

The family Sergestidae provide a unique system for studying the evolution of bioluminescence, with species possessing one of three distinct forms of photophores. This study capitalizes on molecular data to construct a genus-level phylogeny of sergestid shrimp. “Genome skimming” was implemented, capturing mitochondrial genomic data across 19 species. Additional individuals were incorporated through Sanger sequencing of four partial gene regions. The -sergestes group of genera was recovered as non-monophyletic, with the -sergia group of genera being recovered as monophyletic. Ancestral state reconstructions of light organ type indicate the organs of Pesta photophore is the ancestral state for the …

Exploring Epigenetics As A Tool For Population Assessment And Conservation In Large Marine Predators, Andria Paige Beal

FIU Electronic Theses and Dissertations

Worldwide, many large marine predator populations are in decline. These populations can be difficult to study due to the extensive home ranges and migration patterns often exhibited by these species. Molecular tools are therefore necessary to measure specific parameters on these populations that would otherwise be nearly impossible to obtain. This dissertation pioneers the use of environmental epigenetic approaches for that purpose, and specifically the epigenetic modification known as DNA methylation, using sharks and small cetaceans as model organisms. This work is organized into five chapters. Chapter I is an introductory chapter that lays out the fundamentals of environmental epigenetics …

Invasion Ecology And Response To Fire Of The Nonnative Fern Lygodium Microphyllum In The South Florida Everglades, Nicole Sebesta

FIU Electronic Theses and Dissertations

Lygodium microphyllum (Old World Climbing Fern (OWCF)) is a climbing fern native to tropical and subtropical regions of Australia, Asia, and Africa. First introduced to Florida as an ornamental in the 1960s, the fern has become a serious invasive in numerous Florida habitats, severely degrading native herbaceous and woody vegetation and altering fire behavior. One area with the greatest increase in OWCF cover is the sawgrass marsh of southern Everglades National Park (ENP), where prescribed fire is used for both maintenance of sawgrass marshes and management of OWCF infestations. However, the efficacy of OWCF control using fire in this habitat …

Functional Regionalization In The Fly Eye As An Adaptation To Habitat Structure, Carlos A. Ruiz

FIU Electronic Theses and Dissertations

With over 150,000 described species, flies constitute one of the most species-rich groups of animals on earth, and have managed to colonize almost every corner of it. Part of their success comes from their amazing flying skills, which are strongly tied to their visual capabilities. To navigate fast and accurately through their habitats, they must be able to process the inordinate amounts of visual information necessary to sort obstacles, avoid predators and remain on course. Surprisingly, despite their tiny brains, flies have no problem in processing all that information to generate correcting maneuvers in just about 30 ms. To this …

Growth Of Diatom Fistulifera Alcalina In Bacterial Co-Culture And Comparative Mitogenomics Of Fistulifera Species, Erwin David Berthold

FIU Electronic Theses and Dissertations

Diatoms are excellent biological models of growth and intracellular oil generation. The productivity and compounds of diatoms, especially oils, support aquatic food chains and human medical and industrial needs. The qualities that made diatoms prolific producers, specifically diatom physiological features such as growth rates with intracellular lipid storage in alkaline environments, are however poorly understood. Another physiological aspect that remains unexplored is the effects of bacteria on the growth and lipid production of alkaliphilic diatoms. More studies, especially co-cultures, are needed for advances in diatom biology and strain performance for the algal biotechnological field. Besides physiology, diatom genetics using next-generation …

A Comparative Genomics Exploration Of Inter-Partner Metabolic Signaling In The Coral-Algal Symbiosis, Katherine E. Dougan

FIU Electronic Theses and Dissertations

At the foundation of coral reef ecosystems is the symbiosis between the coral host and its microbial community, particularly its photoautotrophic algae from the family Symbiodiniaceae. As a symbiosis centered around nutritional exchange, determining the mechanisms involved in the maintenance of this cooperative exchange is central to understanding how it breaks down. As the nutritional transfer primarily consists of sugars, this work first focuses on the cnidarian insulin signaling pathway, an evolutionarily important metazoan pathway involved in diverse functions, most notably metabolism. This dissertation unveiled 360 putative cnidarian insulin-like peptides (cnILPs) from existing transcriptomic datasets, where they were previously missed …

Connections In The Underworld: A Morphological And Molecular Study Of Diversity And Connectivity Among Anchialine Shrimp., Robert Eugene Ditter

FIU Electronic Theses and Dissertations

This research investigates the distribution and population structure of crustaceans, endemic to anchialine systems in the tropical western Atlantic focusing on cave-dwelling shrimp from the family Barbouriidae. Taxonomic and molecular tools (genetic and genomic) are utilized to examine population dynamics and the presence of phenotypic hypervariation (PhyV) of the critically endangered species Barbouria cubensis (von Martens, 1872). The presence of PhyV and its geographic distribution is investigated among anchialine populations of B. cubensis from 34 sites on Abaco, Eleuthera, and San Salvador, Bahamas. Examination of 54 informative morphological characters revealed PhyV present in nearly 90% (n=463) of specimens with no …

Investigating The Population Dynamics Of An Avian Apex Predator Across An Urban Gradient, Donna Marain

FIU Electronic Theses and Dissertations

Predators are often the focus of conservation efforts. They can be useful sentinel species, umbrella species, and flagship species. Predators can also be the first guild lost when ecosystems are under stress, especially from anthropogenic land-use change. Avian predators (raptors) can be an exception to this trend, filling the role of apex predators across the urban gradient. South Florida contains the Everglades ecosystem and one of the fastest growing human populations in the country. In the current study, I investigated the population dynamics of South Florida’s most abundant hawk: the Red-shouldered Hawk (Buteo lineatus, RSHA) across the urban …

Phylogenetic And Transcriptomic Analyses Of Vision In Two Cave Adapted Crustaceans, Asellus Aquaticus (Isopoda: Asellidae) And Niphargus Hrabei (Amphipoda: Niphargidae)., Jorge L. Perez Moreno

FIU Electronic Theses and Dissertations

The unique characteristics of aquatic caves and of their predominantly crustacean biodiversity nominate them as ideal study subjects for evolutionary biology. The present dissertation capitalizes on a perfect natural experiment, the Molnar Janos thermal cave system in Budapest, Hungary. This intricate freshwater cave system and the immediately adjacent Malom Lake present the ideal opportunity to address questions of colonization, adaptation, and evolution. Despite marked environmental differences between the cave and surface waters, both localities are inhabited by natural populations of two emerging model cave species, the isopod Asellus aquaticus and the amphipod Niphargus hrabei. In the present dissertation, I …

Understanding, Quantifying, And Reducing Bias In Fisheries-Independent Visual Surveys, James Kilfoil

FIU Electronic Theses and Dissertations

Understanding spatiotemporal changes in populations is vital for conservation managers to assess current recovery efforts, determine future conservation priorities, and forms the basis to explore complex ecological questions. In fisheries, these data have traditionally been collected using fisheries-independent surveys that rely on extractive sampling practices (e.g., longlines, gillnets, trawls). However, with the growing availability of low-cost, high-definition cameras, researchers are increasingly using visual surveys as a non-invasive alternative. Camera surveys have a number of advantages including their archivable data, and offer insights into species habitat use and behavior. However, the use of cameras has a number of inherent biases. Understanding, …

The Metabolic Ecology Of Tropical Amphibians Across An Elevational Gradient In The Andes Of Southeastern Peru, Michael R. Britton

FIU Electronic Theses and Dissertations

Metabolism is a fundamental biological process that determines the rate at which organisms process energy and materials, and determines the availability of resources for growth, maintenance and reproduction. Metabolic rates scale across levels of organization from cells to whole organisms and affect population, community, and ecosystem processes. Anthropogenic climate change and other environmental changes are predicted to have major impacts on the energetics of organisms that will be mediated through metabolic physiology. Tropical ectotherms, such as amphibians, may be among the most vulnerable to metabolic impacts of climate change as a result of being ectothermic, having high thermal sensitivity, and …

Mechanisms For The Persistence Of The Coral Holobiont In The Warming Oceans Of The Anthropocene, Daniel G. Merselis

FIU Electronic Theses and Dissertations

Coral Reefs are rapidly deteriorating in response to an onslaught of human-mediated stressors. Just one stressor alone, climate change, may extirpate coral reef ecosystems within a human lifetime, threatening societal and ecological catastrophe. Reef-derived ecosystem services are crucial for sustenance, coastal protection, and economic prosperity in over 100 countries. Near-term human decisions will determine whether reef-corals, the ecosystems they engineer, the 25% of marine biodiversity they support, and the human communities that depend upon them can be protected. My dissertation aims to characterize the potential for corals' adaptive mechanisms to facilitate their continued survival- information which will only represent hope …

Evolutionary Expansions And Neofunctionalization Of Ionotropic Glutamate Receptors In Cnidaria, Ellen G. Dow

FIU Electronic Theses and Dissertations

Reef ecosystems are composed of a variety of organisms, transient species of fish and invertebrates, microscopic bacteria and viruses, and structural organisms that build the living foundation, coral. Sessile cnidarians, corals and anemones, interpret dynamic environments of organisms and abiotic factors through a molecular interface. Recognition of foreign molecules occurs through innate immunity via receptors identifying conserved molecular patterns. Similarly, chemosensory receptors monitor the environment through specific ligands. Chemosensory receptors include ionotropic glutamate receptors (iGluRs), transmembrane ion channels involved in chemical sensing and neural signal transduction. Recently, an iGluR homolog was implicated in cnidarian immunological resistance to recurrent infections of …

Factors Affecting Green Turtle Foraging Ecology Across Multiple Spatial Scales, Elizabeth Rose Whitman

FIU Electronic Theses and Dissertations

The hierarchical levels at which resource selection occurs can have important consequences for individual and population energy budgets and structure the impacts of a forager on its ecosystem. Assessing factors affecting resource selection of large marine herbivores across scales is important because of their potentially large impacts on seagrass community dynamics and historical and current changes in their population sizes and those of their potential predators. I explored the factors (predation risk, resource abundance, quality and identity) affecting resource use of large marine herbivores (green turtles, Chelonia mydas) from the scale of habitat patches to forage species within patches. …

Spatial And Temporal Patterns Of Arctic Nearshore Fish Community And Food Web Structures, Mark B. Barton

FIU Electronic Theses and Dissertations

Climate change and increasing anthropogenic activities are causing rapid changes to environmental and ecological processes in the Arctic Ocean. To better understand these changes, scientists have increased research efforts in these regions, but to date the number of studies on Arctic nearshore habitats are lacking. My dissertation responds to the paucity of information and investigates patterns in Arctic nearshore fish communities and food webs to gain insight to how these ecosystems may shift as these changes continue. I used multivariate statistical analysis to examine patterns in community structure and composition to determine that Arctic nearshore fish communities are largely driven …

Quantitative Spatial Upscaling Of Categorical Data In The Context Of Landscape Ecology: A New Scaling Algorithm, Daniel Gann

FIU Electronic Theses and Dissertations

Spatially explicit ecological models rely on spatially exhaustive data layers that have scales appropriate to the ecological processes of interest. Such data layers are often categorical raster maps derived from high-resolution, remotely sensed data that must be scaled to a lower spatial resolution to make them compatible with the scale of ecological analysis. Statistical functions commonly used to aggregate categorical data are majority-, nearest-neighbor- and random-rule. For heterogeneous landscapes and large scaling factors, however, use of these functions results in two critical issues: (1) ignoring large portions of information present in the high-resolution grid cells leads to high and …

Evolutionary And Population Dynamics Of Crustaceans In The Gulf Of Mexico, Laura Timm

FIU Electronic Theses and Dissertations

Evolution occurs and can be conceptualized along a spectrum, bounded on one extreme by the relationships between deep lineages – such as phyla, classes, and orders – and on the other by the molecular dynamics of operational taxonomic units within a species, defined as population genetics. The purpose of this dissertation was to better understand the evolutionary and population dynamics of crustaceans within the Gulf of Mexico. In the second chapter of my dissertation, I provide a guide to best phylogenetic practice while reviewing infraordinal relationships within Decapoda, including the promise held by next-generation sequencing (NGS) approaches such as Anchored …

The Adaptive Evolution Of Herbivory In Freshwater Systems, Jessica Lynn Sanchez Montelongo

FIU Electronic Theses and Dissertations

Herbivory is thought to be nutritionally inefficient relative to carnivory and omnivory. But, herbivory evolved from carnivory in many lineages, suggesting that there are advantages to eating plants. To understand the adaptive significance of the transition from carnivory to herbivory, I proposed five hypotheses for the adaptive evolution of herbivory and reviewed the current freshwater literature to identify conditions where eating plants might be adaptive over eating animals. I tested three of these ideas (Suboptimal Habitat, Heterotroph Facilitation, and Lipid Allocation) using the herbivorous Sailfin Molly (Poecilia latipinna)and identified each as a potential mechanism for the evolution of …

A Confluence Of Invasion, Behavioral, And Theoretical Ecology: What Drives Ephemeral Metacommunity Re-Assembly?, Jesse Ryan Blanchard

FIU Electronic Theses and Dissertations

Metacommunity theory has been particularly useful in understanding the way spatially structured communities assemble. Both niche and neutral processes are known to influence metacommunity assembly, and the relative influence of each depends on the level of dispersal-limitation. Contemporary trait-based analyses of metacommunity assembly have enhanced our understanding of these processes. Of the traits investigated, individual personalities have received the least attention, but have been suggested to be drivers of metacommunity assembly model parameters, such as dispersal tendencies and patch density. I address this topic from three angles, three chapters, in this dissertation. First, I used a three-year field survey of …

Patterns Of Carbon Metabolism, Storage, And Remineralization In Seagrass Ecosystems, Jason Lee Howard

FIU Electronic Theses and Dissertations

Coastal marine sediments have recently been identified as globally important stocks of organic carbon (C_org) that, if compromised, could significantly exacerbate global greenhouse gas emissions. While resource managers and policy makers are eager to incorporate this ecosystem service into seagrass ecosystem valuation frameworks, similar to those already in existence for terrestrial forests, there has been insufficient information regarding how environmental conditions and seagrass ecology control carbon storage. These include the influence of the seagrass to the production and preservation of soil organic matter, the fate of stored carbon following conversion of coastal wetlands, and the interactions between organic …

Drivers And Mechanisms Of Peat Collapse In Coastal Wetlands, Benjamin J. Wilson

FIU Electronic Theses and Dissertations

Coastal wetlands store immense amounts of carbon (C) in vegetation and sediments, but this store of C is under threat from climate change. Accelerated sea level rise (SLR), which leads to saltwater intrusion, and more frequent periods of droughts will both impact biogeochemical cycling in wetlands. Coastal peat marshes are especially susceptible to saltwater intrusion and changes in water depth, but little is known about how exposure to salinity affects organic matter accumulation and peat stability. I investigated freshwater and brackish marsh responses to elevated salinity, greater inundation, drought, and increased nutrient loading. Elevated salinity pulses in a brackish marsh …

Recovery Of Amphibian And Reptile Communities During Tropical Secondary Forest Succession, Michelle E. Thompson

FIU Electronic Theses and Dissertations

The extensive clearing and modification of natural systems from anthropogenic activities is a pressing global concern. Forest habitats and animal communities within forests are among the most highly impacted, globally. Forest destruction has been repeatedly documented as a driver of biodiversity loss. However, little is known about how animal communities respond when altered landscapes are abandoned and left to regenerate into secondary forests. It is thought that the regrowth of secondary forests may help reverse biodiversity loss by restoring habitats to similar conditions as prior to land conversion. Of the forest cover that remains, over half is secondary forest, and …

A Historical Floristic Inventory Of Pine Rockland Fabaceae (Leguminosae), Adel L. Pena

FIU Electronic Theses and Dissertations

The objectives of this study were to investigate temporal changes in the diversity of pine rockland Fabaceae, induced by anthropogenic factors. Herbarium collections spanning 170 years were used to analyze species frequency and richness. The results indicated temporal fluctuations in diversity with frequency of native species highest previous to the year 1920, and exotic-invasive species richness peaking after the 1960s. The accompanying species list resulting from the inventory included 122 Fabaceae species, in 56 genera, with an additional 19 species not previously listed for pine rocklands. The results emphasize the damage caused by early and deliberate introductions of exotic species, …

Phenomenological And Molecular Basis Of The Cnidarian Immune System, Tanya Brown

FIU Electronic Theses and Dissertations

Coral reefs are one of the most diverse ecosystems on the planet due partially to the habitat structure provided by corals. Corals are long lived organisms that can live for hundreds of years and as a result growth of many species is very slow. As a result of this, recovery of corals from disease outbreaks is very slow and difficult and therefore the ecosystem is deteriorating rapidly. Due to this increase in disease and its detrimental effect on coral reefs, it has become imperative to study how corals respond to disease outbreaks. The response of the coral to pathogens is …

Jewels For Dollars: Native And Nonnative Freshwater Fish Interactions In A Stressful Dry Down Environment, Vanessa Trujillo

FIU Electronic Theses and Dissertations

Vertebrate populations are subjected to novel anthropogenic stressors that are expected to multiply exponentially in the future. Introductions of nonnative species and human-altered hydrology are among these stressors to native species communities. The Rocky Glades, located in Everglades National Park, may serve as a population sink for native species that typically do not survive the altered hydrology of the dry season, and as a source of nonnative species that may be better adapted to chronically stressful conditions. In the seasonally-flooded Everglades, the nonnative African Jewelfish invaded in the 1960s and has since shown rapid range expansion. African Jewelfish are aggressive …

Green Sea Turtles (Chelonia Mydas) In Bermuda Exhibit An Ontogenetic Diet Shift Despite Overexploitation Of Resources In Their Developmental Habitat, Claire Margaret Burgett

FIU Electronic Theses and Dissertations

Green sea turtles in Bermuda are overgrazing the seagrasses on which later life stages are thought to specialize. I hypothesized that larger green turtles in Bermuda would display individual diet specializations during seagrass scarcity. Stable isotope methods were used to determine the diet composition of green sea turtles from the Bermuda Platform as a function of size class and in turtles captured in successive years. Individual turtles had a wide range of diets, however, the variation in diets was driven by differences among size class rather than within the size classes of larger turtles, indicating that green turtles undergo a …

Examining Movement And Habitat Selection Of Everglades Fishes In Response To Seasonal Water Levels, Gregory J. Hill

FIU Electronic Theses and Dissertations

Fish distribution patterns and seasonal habitat use play a key role in the food web dynamics of aquatic ecosystems, including the Florida Everglades. In this study I examined the fine scale habitat shifts and movements of spotted sunfish, Lepomis punctatus across varying seasons and hydrologic conditions using in-situ field enclosures and Passive Integrated Transponder (PIT) systems. Data on fish use of three dominant Everglades marsh habitats and activity level were recorded continuously from January to August, 2015. Fish were more active and had the highest use of higher elevation habitats when water levels rose during an experimental reversal in mid-April. …

The Effects Of Artemisia Derived Natural Products On Adipogenesis, Steven Abood

FIU Electronic Theses and Dissertations

For the first time in human history, more people worldwide suffer from obesity than are undernourished. Numerous health complications are associated with obesity including cardiovascular disease, Type 2 Diabetes, cancers of reproductive tissues, stroke, depression, anxiety disorders, and Alzheimer’s disease. A deeper understanding of the anti-adipogenic effects and mechanism of action of sesquiterpene lactones may have pharmacological import in the continuing search for therapeutic modalities to ameliorate the effects of this global obesity epidemic.

Dehydroleucodine (DhL), 11,13-dihydro-dehydroleucodine (DH-DhL), and dehydroparashin-B (DhP), sesquiterpene lactones extracted from or derived from compounds extracted from Artemisia douglasiana, were investigated for their anti-adipogenic effects …

Screening Of Plants For Antibacterial Properties: Growth Inhibition Of Staphylococcus Aureus By Artemisia Tridentata, Steven Ross Eichelbaum

FIU Electronic Theses and Dissertations

Drug-resistant pathogenic and opportunistic bacteria are increasing in occurrence and prevalence, and pose a dangerous threat to human health. In the search for novel antibiotics with which to combat this threat, plants, specifically those used in traditional medicine with ascribed antibacterial properties, offer a promising and potentially vast source of such therapeutic compounds. The purpose of this study was therefore to screen chemical extracts created from various plant species for antibacterial properties versus pathogenic bacterial species. In the course of these antibacterial assays, we successfully identified a methanol extract derived from Artemisia tridentata tridentata plant material as capable of inhibiting …