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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 …

Population Ecology Of A Caribbean Epiphyte Trichocentrum Undulatum (Orchidaceae): Defining Habitat And The Effects Of Herbivory And Hurricanes At Its Peripheral And Core Range, Haydee Borrero

FIU Electronic Theses and Dissertations

Population ecology studies are central to species conservation. My dissertation focused on the Florida state-listed endangered orchid, Trichocentrum undulatum at its northern-most range in the Everglades National Park (ENP), Florida and multiple populations throughout its core range in Cuba. Through surveying populations of T. undulatum across this range from 2013-2021, I made a new reporting on the occurrence of a specialized insect herbivore, Melanagromyza miamensis in Cuba (Chapter 1). This flower-crippling herbivore was previously known only in the ENP. With this discovery I assess the intensity and impacts of this herbivore, as well as others on T. undulatum across the …

Evaluating Changes In Visible To Short-Wave Infrared Spectral Reflectance Of Arctic Mosses In Response To Experimental Drying To Find The Best Predictors Of Moisture Content, Steven L. Unger

FIU Electronic Theses and Dissertations

Mosses are a dominant understory component in the Arctic and because of sparse canopy cover, contribute to spectral signals used in remote sensing estimates of various ecologically important characteristics such as productivity, phenology, and vegetation mapping. However, little is known about their contributions to community level spectra or how moisture content influences those spectral signals. Unlike vascular plants, mosses cannot actively regulate moisture content and are highly susceptible to desiccation. Previous research has shown that moss reflectance is sensitive to tissue moisture content. Here, a lab-controlled drying experiment was conducted to identify the best spectral predictors of moisture content of …

Drivers Of Extracellular Polysaccharide Production By A Mat-Forming Diatom, Kaitlin A. Stansbury

FIU Electronic Theses and Dissertations

Microbial biofilms are held together by extracellular polymeric substances (EPS), which can be secreted by many organisms. EPS production can facilitate intercellular communication and inter-guild microbial mutualisms, intraspecific gamete exchange, nutrient sequestration, and desiccation resistance. Benthic microbial mats (periphyton) of the Florida Everglades and other karstic wetlands contain abundant EPS generated by mat-producing filamentous blue-green algae and many other species of mat-dwelling algae, cyanobacteria, and bacteria, including the most abundant Everglades diatom, Mastagloia calcarea. The benthic diatom genus Mastogloia is characterized by several morphological and physiological features that foster production of a ‘halo’ of EPS around the frustule, but the …

Reconstructing Cyclical Browning In A Subtropical Lake From Diatoms, Meredith Emery

FIU Electronic Theses and Dissertations

Lakes are browning globally from increased inputs of colored dissolved organic carbon (cDOC) driven by climate and land-use change. Browning changes lake ecosystems, especially through reductions in water transparency. I used long-term limnological and plankton records and upper surface sediment diatom assemblages to infer a ~1600-year history of browning from diatom assemblages in a 166 cm core from a subtropical, oligotrophic lake known to experience cyclical browning related to climate oscillations. Diatom assemblages were strongly regulated by cDOC-driven transparency fluctuations in a 14-year plankton dataset (modern model, R² = 0.62) and in the upper 35 cm of sediments corresponding …

Functional Strategies Of Tree Fine-Roots In Relation To The Soil Environment And Microbiome: Variaiton In Root Morphology, Tissue Chemistry And Physiology, James Aaron Hogan

FIU Electronic Theses and Dissertations

Tree root systems have evolved multidimensional functioning, specializing in water and nutrient acquisition via different strategies. Root functional strategies vary among tree species and are adapted to the abiotic and biotic soil environment. This dissertation explores how three facets of root system functional strategies – morphology and chemistry, biotic associations with fungi, and respiration rates – vary within and among tree species along environmental gradients. Chapter one examines how root system morphology varies with forest succession and soil environment in a tropical forest of Hainan, China, finding that root systems had larger diameters and fewer root tips in the younger …

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 …

Quantifying How Coastal Flooding And Stormwater Runoff Drive Spatiotemporal Variability In Carbon And Nutrient Processing In Urban Aquatic Ecosystems, Matthew A. Smith

FIU Electronic Theses and Dissertations

Coastal river networks alter the transport and transformation of dissolved organic carbon (DOC) and dissolved organic matter (DOM), which can vary in concentration and composition across spatiotemporal scales. Given climate-induced shifts in rainfall and tidal variation in low-lying coastal regions, there is an increasing need to quantify effects of flooding on biogeochemical cycling. Specifically, urban flooding is becoming increasingly common due to biophysical alterations to hydrology from urbanization and climate change. Urban ecosystems have been characterized as having a distinct biogeochemistry compared to other systems, largely due to increased frequency and magnitude of riverine and coastal flooding. Consequently, the role …

Invasion Genetics Of The Non-Native Geckos Phelsuma Grandis Gray 1870 And Gekko Gecko (Linnaeus 1758) In Southern Florida, Usa, Thomas William Fieldsend

FIU Electronic Theses and Dissertations

Biological invasions cause tremendous damage to ecosystems, economies, and human livelihoods worldwide. Florida is home to more established non-native species of reptiles and amphibians than anywhere else on Earth, many of which cause substantial harm to native biodiversity and human well-being. The relatively new discipline of invasion genetics promises to significantly improve the understanding, prediction, prevention, and management of biological invasions. The purpose of this dissertation is to utilize invasion genetics techniques to further understanding of the patterns and processes of biological invasions, especially as they pertain to Florida’s destructive and diverse non-native squamate reptile assemblage. In the first phase …

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 …

Comparison Of Modern And Mid-Holocene Benthic Foraminifera To Assess Recent Environmental Change In Almirante Bay, Caribbean Panama, Maria N. Gudnitz

FIU Electronic Theses and Dissertations

This study used the diversity and distribution of benthic foraminiferal assemblages of Almirante Bay, Caribbean Panama, as environmental proxies to compare modern coral, seagrass and mangrove habitats to mid-Holocene coral reef facies on the island of Isla Colón, to investigate both natural and human-influenced changes.

The modern study associated species and assemblage characteristics with environmental conditions related to degraded water quality. Assemblages were fairly similar among neighboring habitats but differed in species proportions, while several stress-tolerant taxa might indicate eutrophic conditions. Diversity appeared to be regionally controlled by freshwater input irrespective of habitat type, was generally lower near the mainland …

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 …

Long-Term And Seasonal Drivers Of Phytoplankton Assembly In A Subtropical Monomictic Lake, Kristy Lee Sullivan

FIU Electronic Theses and Dissertations

Seasonal phytoplankton dynamics in lakes are highly sensitive physicochemical changes in the water column. As climate-driven frequency and variability of precipitation increases, lakes may experience increased inputs of allochthonous organic matter and nutrients through pulsed rain events. The resultant effects of lake physicochemistry on phytoplankton seasonal succession and assemblage are poorly understood. In the current study, the phytoplankton assemblage of a subtropical monomictic lake was examined in the context of natural interannual oscillations in allochthonous dissolved organic carbon and nutrient inputs resulting in prolonged clear-water and dark-water phases over a 14-year period. Differences in water clarity and nutrient concentrations among …

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 …

Systematic Studies In Myrtaceae Of The Greater And Lesser Antilles, Jonathan A. Flickinger

FIU Electronic Theses and Dissertations

The Myrtaceae, or myrtle family, are a group of flowering trees and shrubs represented in the Americas by over 2000 species of the predominantly Neotropical tribe Myrteae. Recent progress on the challenging systematics of the group has been achieved through molecular phylogenetics, but few of the almost 500 species endemic to the islands of the Greater and Lesser Antilles in the Caribbean have been included in either phylogenetic or revisionary studies. The purpose of my dissertation is therefore to contribute to the description and phylogenetic classification of Antillean Myrtaceae. The first study describes Eugenia walkerae, a new species of …

Structure, Control, And Communication Of Collective Animal Behavior In Dynamic Environments, Ivan Ignacio Rodriguez-Pinto

FIU Electronic Theses and Dissertations

Collective behavior in animal aggregations is highly complex and spans multiple spatial scales, across a wide range of environmental conditions. In socially active fish, aggregation into schools is a widespread adaptation that confers a variety of safety benefits. The emergent patterns exhibited by collectively behaving fish schools may be influenced by biotic (i.e. predation) or abiotic (i.e. habitat complexity, turbidity) factors in the local environment. Our knowledge of the ways and extent to which environment variability affects schooling behavior at the collective level is currently limited. In this dissertation, I investigated whether environmental factors influenced the collective behavior of fish …

Beyond Predation: How Do Consumers Mediate Bottom-Up Processes In Ecosystems?, Bradley Austin Strickland

FIU Electronic Theses and Dissertations

By eating and scaring prey, predators can exert strong effects on communities and ecosystems. In addition, some animals may physically alter habitats and may recycle nutrients through digestion, both of which affect resources available to producers. Bottom-up effects initiated by large predators have not been well-studied and could prove to be important for understanding food webs and how ecosystems function. American alligators (Alligator mississippiensis) are abundant mobile predators that are capable of engineering aquatic habitats by moving organic material across ecosystem boundaries and creating and maintaining alligator ponds. In this dissertation, I documented the scale of ecological impacts …

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 …

Taking Apart The Time Machine: Investigating Space-For-Time Substitution Modeling In The Florida Everglades, Theresa Kelly Brown

FIU Electronic Theses and Dissertations

Space-for-Time substitution modeling has been used with increasing frequency to identify functional relationships between environmental drivers and ecological responses. I investigated the use of space-for-time substitution as a null model and beta diversity as a validity test for this null model in the Greater Everglades aquatic metacommunity. I began by conducting a literature review and analysis to investigate the suitability of the space-for-time substitution method as a null model. I then analyzed beta diversity of the Greater Everglades aquatic metacommunity through a sums-of-squares approach. Finally, I tested for correlation between the beta diversity analysis and the space-for-time models. Results indicate …

Incorporating Early Life History And Recruitment In Analysis Of Population Dynamics Of Wetland Fishes, John Vincent Gatto

FIU Electronic Theses and Dissertations

Hydrological variation is believed to be the major abiotic factor influencing fish recruitment in floodplain ecosystems. However, past studies fail to address the impact of hydrology on the three major drivers of recruitment: age-specific growth and mortality, and dispersal. I examined long-term recruitment dynamics for six fish species inhabiting the Everglades by addressing the impact of hydrology on these important characteristics. I then linked these changes to annual fluctuations in population size.

Before interpreting time-series data on recruitment, I evaluated the impact of size-selective bias from sampling gear on our interpretation of hydrological drivers of recruitment. Analyses revealed that individuals …

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 …

Effects Of Phosphorus On Benthic Diatom Assemblage Network Structure, Eric M. Massa

FIU Electronic Theses and Dissertations

Ecological network analysis helps identify how relationships among species differ over time and across sets of species. Microbial assemblages are ideal for evaluating changes in species interactions due to environmental changes because they are speciose and respond at multiple scales. To determine how phosphorus limitation influences diatom network structure, I analyzed relationships among 257 species of diatoms from benthic microbial (periphyton) mats from 10 years of annual samples from 136 sites. Expected evidence of changes in network structure in response to periphyton TP were not found, likely due to species replacement with increased TP. Analysis of species connection distributions and …

Cavity Nest Webs As A Template For Studying Non-Trophic Interactions In Invasion Ecology, Joshua M. Diamond

FIU Electronic Theses and Dissertations

Invasive exotic animals are considered destructive forces in cities for preying on and competing with native species. I examined an aspect of competition from a different perspective, focusing on the role of Miami’s rich exotic bird assemblage in its cavity nest web, where a supply of woodpecker-created cavity nests limited by urbanization is the focal point of competition. We located 967 nest trees with 1,864 cavities and determined that woodpeckers successfully nested in this tropical urban region by exploiting standing dead palms (snags). Native upland forests were the most important cover type for woodpeckers but planted landscapes like parks and …

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 …