Coarse outcomes of prescribed fires are well-understood, but fine scale impacts on many assemblages are still unknown. When fire approaches, animals escape to unburned areas, hide in place, or are killed by fire. Treefrogs are unique in their use of trees for most of their adult nonbreeding activities. This reliance on uplands and three-dimensional landscape composition makes them a great model to study prescribed fire impacts. We focused analyses on an upland flatwoods specialist comprising 99% of our captures, the pinewoods treefrog Dryophytes femoralis. We assessed this species' responses to prescribed fire using two separate before-after-control-impact replicated field experiments in a Central Florida pine flatwoods landscape. In Study I, we assessed fire impacts on population and movement in canopies over six months (N = 76 frogs, 198 recaptures). We used single rope technique and climbing equipment to set PVC pipes as treefrog refugia at 3 m, 6 m, 9 m, and 9+ m in twelve longleaf pines, Pinus palustris, across four plots, two of which had fires scheduled during the study. Study II evaluated frog population changes in uplands in response to prescribed fires (N = 1804 frogs, 1790 recaptures). We collected 27 months of mark-recapture data by checking 240 open PVC pipes at 2 m in longleaf pines across eight plots with fires prescribed during the study. Using mark-recapture and mixed generalized linear models with Bayesian framework, we modeled abundance, survival, recapture, and vertical movement parameters. We found the prevailing mechanism for resiliency to fire for pinewoods treefrogs was refugia up pines, then recolonization of lower layers when they regreen post-fire. This finding substantiates others' conclusions that structural integrity of the community is key to sustaining native biodiversity. Future work and management should increase consideration of the three-dimensional structure of the habitat when developing burn prescriptions and study designs.

Amazonian freshwaters host the most diverse ichthyofauna in the world but the ecological mechanisms that generate and regulate this diversity are poorly known. I performed the first comparison of spatial and temporal patterns of fish community diversity among the four primary aquatic habitats of the Amazon (major rivers, floodplains, lowland terra firme streams, and upland shield streams) and among the three distinct chemical water types in Amazon river-floodplain systems (low-nutrient blackwaters and clearwaters, and high-nutrient whitewaters). To minimize confounding influences of geographical variation in species ranges, my study targeted one of the few parts of Amazonia (near Santarém, Brazil) where all four habitats and all three river-floodplain water types occur in close proximity. In the first of three chapters, I compare diversity and biomass between blackwater, clearwater, and whitewater rivers and floodplains. My results provide the first support for positive species-energy and biomass-energy relationships across multiple aquatic habitat types from the same biome and region. In Chapter 2 I compare patterns of temporal beta-diversity, and beta-deviations from null model simulations, to demonstrate that species turnover is positively correlated to seasonality and hydrological connectivity among the four Amazonian habitats types but is uninfluenced by water type. In Chapter 3 I compare up-river transects from the common confluence of a blackwater, Clearwater, and whitewater river to infer that abrupt gradient of water chemistry act as major barriers to fish dispersal. My results have important implications for biodiversity monitoring and conservation planning in the increasingly threatened aquatic habitats of the Amazon basin.

Recent work indicates that the Y-chromosome of the fruit fly Drosophila melanogaster can influence gene regulation on the autosomes and X chromosome. This newly discovered function of the Y has the potential to dramatically shape the regulatory evolution of numerous genes that reside throughout the genome; even for genes that code for both male and female traits. Given that the mechanism underlying the Y-linked influence on gene expression in D. melanogaster appears to exist in other independently evolved heterogametic sex chromosomes, the evolutionary implications of Y-linked regulatory variation (YRV) deserves to be explored. These implications include the potential for Y-chromosomes to facilitate the adaptive evolution of sexually dimorphic gene expression, and the potential for the Y to constrain evolutionary rates in both males and females (depending on the nature of the YRV effect). Unfortunately, the evolutionary implications of this potentially widespread and significant phenomenon have yet to be explored. My dissertation addresses this knowledge gap by determining the influence YRV has on the evolution of autosomally coded traits in D. melanogaster. First, we address the potential for selection to shape YRV by determining if YRV (i) exists within natural populations (i.e. where natural selection operates), and (ii) has any influence on male fitness-related autosomal traits. Second, we address if YRV can facilitate the adaptive evolution of sexually dimorphic gene expression by testing for the presence of Y-linked additive genetic variation. To this end, we investigate the physiological properties of select Y-chromosomes across multiple genetic backgrounds. Third, we address if YRV can constrain adaptive evolution for autosomally coded traits by employing artificial selection on replicate populations that contain either multiple Y-chromosomes (i.e. contain YRV) or only a single Y-chromosome (no YRV). The following studies present evidence that YRV does exist within populations where natural selection operates. We show significant levels of YRV on X-linked and autosomal immune gene expression in wild caught D. melanogaster from a single natural population. Furthermore, YRV effects on immune related genes show a significantly positive correlation to a male fly's ability to fight an immune challenge (an important aspect of organismal fitness). Estimated physiological properties of YRV support previous interpopulation studies showing strong non-additive effect dependent on the autosomal genetic background with which Y-chromosome's are paired with. Physiological epistasis can manifest as additive genetic variation on a population level, but our experimental evolution study suggest that YRV constrains rather than facilitates the evolution of the autosomal coded geotaxis behavior. Ultimately, this dissertation provides evidence that YRV has the potential to influence how autosomal traits evolve and that population level studies of YRV indicate a potential constraint to the adaptive evolution of autosomal traits. If these trends are common and YRV is a wide spread phenomenon, Y-chromosomes have the potential to influence how autosomal traits evolve.

The Florida manatee (Trichechus manatus latirostris) was recently downlisted federally from "endangered" to "threatened" despite acknowledgments of remaining threats to long term population persistence. Challenges to future manatee conservation include, but are not limited to, increases in frequency of harmful algal blooms, intensifying anthropogenic disturbance, and loss of warm-water habitat. The goals of this dissertation were 1) to assess threats to the manatee via a comprehensive, long-term (1973-2016), retrospective analysis of the manatee rescue and rehabilitation partnership (MRRP) and 2) to use seascape genetics analysis to examine whether abiotic, biotic, or anthropogenic seascape variables could significantly describe genetic distance patterns in space for this genetically depauperate population. Results from the MRRP analysis revealed that anthropogenic threats were the most significant reason for manatees to be rescued and rehabilitated. Manatees rescued due to watercraft injuries spent long periods in recovery before succumbing or being released resulting in significant expense to the rehabilitation system. Additionally, the seascape genetics analysis indicated that watercraft activity best explained spatial genetic patterns in the manatee population. It is established that anthropogenic use of watercraft negative affects manatees through the mechanisms of sub-lethal injury and mortality, and these results suggest there may be further negative impacts via the disruption of population genetic connectivity. Future management practices should seriously consider manatee/vessel interactions as watercraft strikes are costly for management, place pressure on the manatee population, and could disrupt population gene flow with potentially dire consequences. Mitigating anthropogenic impacts on the Florida manatee population is critical for future conservation and should be a primary focus.

Nitrate is the most common ionic form of nitrogen in aquatic ecosystems. Although nitrate is known to affect ecosystems at high levels through eutrophication, hypoxia and loss of biodiversity, it is considered to be physiologically inert to the individual aquatic organism. To test the physiological effects of nitrate on aquatic life, we exposed gill tissue of the Pacific oyster, Crassostrea gigas, to nitrate and characterized changes in protein expression, using a gel-based proteomics approach. Of the 642 protein spots detected, we found that 24 proteins (15 identified) changed expression in response to a 6-hour exposure to nitrate concentrations ranging from 0-73 mg/L, values that characterize highly contaminated surface and ground waters. Proteins changing expression included the oxidative stress proteins thioredoxin and cavortin (a member of the superoxide dismutase family) as well as proteins that are involved in G-protein signaling (Rho-GDI, ADP-ribosylation factor, G-protein ß-subunit), protein homeostasis (heat shock protein 70, prohibitin, calreticulin, and proteasome &#;-type 4 subunit), glycolysis (enolase), transport of hydrophobic molecules (lipocalin) and cytoskeletal arrangements (intermediate filaments and a gelsolin-like adseverin). The most parsimonious explanation for these changes in protein expression assumes that C. gigas reduces nitrate to nitrite and nitric oxide, which reacts with superoxide anions to form the very reactive peroxynitrite. We propose that part of the cellular response to reactive nitrogen species,phagocytic hemocytes inhibit the production of reactive oxygen species, potentially compromising the immune response of oysters to invading pathogens.

Animals that co-occur in sympatry with multiple closely-related species use reproductive mate attraction signals not only to assess the quality of a potential conspecific mate (sexual selection), but also to discriminate conspecifics from heterospecifics (species recognition). However, the extent to which sexual selection and species recognition may interact, or even conflict, is poorly known. Neotropical electric fish offer unrivaled opportunities for understanding this problem. They generate simple, stereotyped mate attraction signals that are easy to record and quantify, and that are well-understood from the neurobiological perspective. Additionally, they live in electrically-crowded environments, where multiple congeners live and reproduce in close proximity. This dissertation reports an investigation of electric signal diversity and reproductive life history in a nine-species assemblage of the electric fish genus Brachyhypopomus from the upper Amazon. A year-long quantitative sampling program yielded a library of electric signal recordings from >3,000 individuals and an accompanying collection of preserved specimens from which suites of informative life history traits were measured. These data were used to understand basic reproductive biology, and to describe sexually dimorphic and interspecific diversity in electric signals. By integrating approaches from ecology, physiology, and evolutionary biology, novel perspectives are provided on: 1. how sexual selection and species recognition interact to shape signal diversity and the occupation of signal space in multi-species animal communities; 2. how extreme seasonal variation in Amazonian ecosystems influences trade-offs in the allocation of reproductive resources – including mate attraction signals, and; 3. how environmental variation shapes general life-history traits in a diverse tropical animal assemblage.

Juvenile dispersal is a life history strategy found across taxa and habitat types. In this dissertation, I examine juvenile dispersal in an evolutionary context and explore the conditions that support high dispersal, which necessitates subsequent ontogenetic habitat shifts. I use a sea turtle study system to evaluate the genetic and behavioral patterns associated with juvenile dispersal and ontogenetic shifts in marine environments. Specifically, I focus on four sea turtle species found in the northeastern Gulf of Mexico in the early life stage known as the 'lost years': green turtles (Chelonia mydas), Kemp's ridleys (Lepidochelys kempii), loggerheads (Caretta caretta), and hawksbills (Eretmochelys imbricata). I use mitochondrial DNA (mtDNA) haplotypes and ocean transport probabilities to estimate contributions from source rookeries to sampling sites in the Gulf of Mexico as well as assess gaps in the available genetic datasets. The mixed stock analyses indicate that the majority of 'lost years' green turtles I sampled originate from nesting beaches along the coast of Mexico, with smaller contributions from Costa Rica and Suriname. More broadly, I identify gaps in available genetic data across species, life stages, and ocean basins, particularly among early juveniles. I use telemetry data to characterize sea turtle 'lost years' movements with respect to the continental shelf and proximity to the coast, potential recruitment to coastal habitats, and passive versus active behavior by using oceanographic surface drifters as a control. The West Florida Shelf is a high-use area, particularly among green turtles and Kemp's ridleys. Finally, I analyze genome-wide single nucleotide polymorphisms to test whether mtDNA haplotype data accurately reflect overall population structure for defining management units. These data provide valuable insight into the elusive 'lost years' juvenile dispersal life stage in sea turtles and fill substantial data gaps impeding management for species conservation.

The purpose of this research was to document the ways in which the pedagogical approaches of technology/engineering design-based learning (T/E DBL) were shown to promote change in concept knowledge of eighth grade mathematics students. A mixed method, sequential explanatory multiple embedded case study was used to determine the significance between the T/E DBL intervention and bivariate measurement data concept knowledge. Whole Group quantitative data analysis indicated a statistical significance between pretest and posttest scores. Qualitative data (Interactive Engineering Journals and semi-structured interviews) analyses for the Sub-Group confirmed that students did possess the bivariate data concept knowledge as documented through quantitative results and those gains were directly related to experiences students had while engaged in the T/E DBL intervention. This research demonstrated that the utilization of T/E DBL in an eighth-grade mathematics classroom has the potential to foster a change in concept knowledge of bivariate measurement data through informed design decision-making in a 21st century problem context. This study can be used as a guide for mathematics educators and curriculum developers implementing T/E DBL pedagogy allowing students to learn through contextual experiences. Future research should explore the utilization of T/E DBL to teach additional mathematical concepts at different grade levels. / Doctor of Philosophy / This research demonstrated that the utilization of technology/engineering design-based learning (T/E DBL) in an eighth-grade mathematics classroom has the potential to increase mathematical concept knowledge through informed design decision-making in a 21st century problem context. Participants were asked to design a solution to a real-world problem which required mathematics concept knowledge in order for students to make decisions about their design. Participants also kept an Interactive Engineering Journal (IEJ) throughout the design challenge. The results of the mathematics pre/posttest taken before and after the design challenge indicated that students increased their mathematical concept knowledge through their experiences during the design challenge. A small group of participants were selected to participate in IEJ analysis and individual interviews. These data confirmed that students did gain mathematical concept knowledge in connection to their experiences during the design challenge. This study can be used as a guide for mathematics educators and curriculum developers implementing T/E DBL pedagogy allowing students to learn through contextual experiences. Future research should explore the utilization of T/E DBL to teach additional mathematical concepts at different grade levels.

The dissertation showcases the effectiveness of explainable machine learning approaches in studying plant ecophysiology and agriculture. It demonstrates the identification and prioritization of ecologically relevant traits using such methods in the genus Helianthus (wild sunflowers). Phenotypic differentiation and interspecific diversification are explored, as well as intraspecific trait variations within Helianthus annuus across different ecological regions. Additionally, the dissertation applies similar methods to assess the impact of historical weather patterns on the agricultural yield of cultivated sunflower at national and regional scales. It also provides yield forecasts under future socioeconomic scenarios, considering the potential effects of climate change on sunflower cultivation. Overall, this work highlights the potential of machine learning coupled with interpretable methods, in analyzing nonlinear and multidimensional biological data, addressing important research questions in plant biology, ecology, and agriculture. The findings contribute to understanding evolutionary predictability, ecological strategies, and the impact of climate change on crop yields.

Stressful environments can commonly be found at the edge of a species range and may be a driver for adaption in suboptimal environments. Furthermore, the edge of a species' range can expand and contract over time, resulting in multiple independent invasions of the same stressful habitat. Elucidating population genetic structure and demographic history can aid in determining the which geologic factors impact range distributions and when climatic changes occurred driving genetic patterns observed in contemporary populations. Moreover, populations at the edge of the species range may adapt to the stressful environments that occur at the range edge and exhibit genetic traits divergent from populations in the core of the species range. In this dissertation, I first examined how a stressor (salinity) has impacted genetic structure and demographic history in a wide-ranging, large semi-aquatic species, the American alligator (Alligator mississippiensis; Chapter 2). I estimated the splitting of genetic clusters and matched them with geologic events of past sea level rise. Then, I tested if coastal populations respond differently to changes in salinity compared to alligators from inland populations (Chapter 3). To do this I randomly placed juvenile alligators from coastal and inland populations in one of three salinities (0, 10, or 20 ppt) for two weeks. I collected behavioral, physiological, and histological datasets and found a habitat by salinity interaction with coastal alligators exhibiting a pattern of increased plasticity relative to inland alligators. In Chapter 4, I hypothesized that coastal and inland alligators would exhibit differentially expressed genes in osmoregulatory organs in response to salt stress. My data supported this hypothesis, and I found that the most differentially expressed genes functioned in signal transduction, metabolic pathways, and secretion. In addition, I found that at high salinities, coastal alligators upregulated genes coding for solute carriers compared to inland alligators. Overall, my dissertation contributed to the study of adaptive evolution by demonstrating that salinity has been a past and current stressor for American alligators. High salinity levels continue to limit the alligator's species range and lead to genetic differentiation among historically isolated regions. Yet, at the same time, I found evidence that coastal populations exhibit incipient adaptation to high salt environments. The patterns I found here are similar to other species that inhabit both freshwater and saltwater environments. As there appears to be evidence of convergent evolution for mechanisms to excrete salt in fully marine reptiles, my dissertation is starting to provide evidence for patterns of convergent evolution among reptiles that similarly use both freshwater and brackish water environments.