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 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.

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.

Billfishes (marlins, spearfishes, sailfishes and swordfish) are one of the fastest and largest marine apex predators, and perhaps their most recognizable attribute is their bill or rostrum. The proposed function for this novel structure has ranged from hydrodynamic enhancement to defensive weaponry. However, the most supported hypothesis for its function has been linked to feeding. Billfishes have been observed to subdue their prey with their rostrum, either stunning or cutting them into pieces before ingestion. Due to their large body sizes and pelagic lifestyles a thorough investigation of the function of this structure has been logistically challenging. The goal of my dissertation is to investigate the role of the rostrum during feeding from a functional, mechanical and morphological standpoint. By the use of interdisciplinary approaches that blend engineering with biology, the function of the rostrum and billfish putative feeding behavior was investigated. By the use of different approaches that involve morphological characterizations, histology, estimation of performance measurements such as bite force and the investigation architectural tradeoffs from geometric morphometrics analysis, my dissertation aims to characterized the role of the rostrum in billfishes as a possible adaptation for feeding. Results showed that the rostrum in billfishes is mechanically capable of acting as a feeding weapon; continuous stress distribution along its length suggest no particular point that could lead to breakage during feeding. Finite element analysis, as well as bending experiments suggest feeding behavior may be species specific and strictly associated with rostrum morphology. While istiophorids may be morphologically suited to strike their prey with a wide range of motions, swordfish appear to be specialized from a mechanical and hydrodynamic standpoint to hit their prey with lateral strikes. Biting performance is relatively low in these top predators compared to other non-billfish species suggesting the rostrum may facilitate prey processing reducing the need for powerful biting. However contrary to my expectations rostrum length was not a predictor of bite force. Skull variation was evident among billfish species. Swordfish, the species with the longest rostrum, had the smallest head and the lowest relative bite force whereas blue marlin, the species with the stiffer, most compact rostrum, had the largest head and one of the greatest relative bite forces. The shortbill spearfish showed a relatively low bite force indicating predatory success in this species may be linked to an extended lower jaw that may facilitate a speed efficient jaw during prey capture. Whether the rostrum in billfishes has evolved as an adaptation for feeding, remains uncertain. However results from this study demonstrate that rostrum material properties, morphology and head architecture, in addition to relatively low biting performance in billfishes, favor a role of prey capture for the rostrum.

Thesis (M.S.)--Rutgers University, 2009. / "Graduate Program in Physiology and Integrative Biology." Includes bibliographical references (p. 39-42).

Thesis (Ph. D.)--Rutgers University, 2008. / "Graduate Program in Physiology and Integrative Biology." Includes bibliographical references (p. 73-79).

Global climate change imposes physiological constraints on marine ecosystems that can alter the distribution of intertidal organisms. In one such instance, the native cold-adapted mussel Mytilus trossulus is being replaced along its southern range by the invasive warm-adapted Mytilus galloprovincialis. These blue mussels occur throughout rocky intertidal zones where they are subjected to greatly varying environmental conditions known to induce oxidative stress. We hypothesize that while under acute stress, related Mytilus congeners undergo a shift in redox potential from NADH-fueled respiratory pathways to pathways producing NADPH as a way to decrease the production of reactive oxygen species (ROS) and provide reducing equivalents to detoxify ROS. Additionally, we hypothesize that sirtuins (SIRT; a family of NAD-dependent deacetylases) might be involved in the regulation of this metabolic transition. To test the latter, a discovery approach will be used to analyze the proteomic response of M. galloprovincialis and M. trossulus to the pro-oxidant menadione, and sirtuin-inhibitors nicotinamide and suramin. Menadione can induce oxidative stress by increasing endogenous peroxide and superoxide radicals, while suramin and nicotinamde both inhibit sirtuin activity. Organisms were exposed to these compounds in filtered seawater for 8 h, followed by a 24.5 h recovery period under constant aeration. A multivariate analysis utilizing 2D-gel electrophoresis and protein identification via mass spectrometry showed that 18% and 17% of all identified protein spots detected demonstrated changes in abundance in M. galloprovincialis and M. trossulus, respectively. Using matrix-assisted laser desorption ionization (MALDI) tandem time-of-light mass spectrometry, we were able to identify 32-41% of proteins, depending on the species. The two Mytilus congeners showed the greatest differences in changes of protein abundance for oxidative stress proteins (including NADP-dependent isocitrate dehydrogenase). Both congeners showed similar effects in response to simultaneous sirtuin inhibition and MIOS for proteins involved in protein degradation (proteasome), cytoskeletal modifications (actin and tubulin), proteins regulating actin filament growth (F-actin capping protein), amino acid metabolism and stress signaling (G-proteins, small G-proteins and MAPK). Results indicate that protein acetylation plays an important role in the oxidative stress response of M. galloprovincialis. More specifically this suggests that sirtuins play an important role in regulating the general stress response in M. galloprovincialis and thus contribute to the greater stress resistance of this species. Furthermore, changes in the abundance of several molecular chaperones suggest a greater effect of sirtuins in regulating the cellular response to heat stress, which could in part explain why this species is more heat-tolerant than the native M. trossulus.

Upon exposure to environmental stressors, amphibians such as Plethodon montanus will release corticosterone (CORT) thus causing a behavioral and physiological response to cope with the stress. Currently, there are several invasive ways of collecting CORT in salamanders. However, these techniques typically require euthanasia of the organism. We hypothesized that exposure of P. montanus to stressful handling conditions will result in elevations of CORT that can be detected through dermal swabbing. To test this, two experiments were conducted which involved swabbing the dorsal side of the trunk before and immediately after exposing P. montanus to two different environmental stressors. The first experiment involved placing P. montanus into a behavioral chamber for twelve hours while the second experiment involved restraining P. montanus in a plastic bag with a damp paper towel for ten minutes. While both experiments indicated an elevation in CORT after the respective treatments, between-replicate variability were high, and the differences were not statistically significant. The results of the first experiment did reveal a stress response when P. montanus were taken out of the chamber. The second experiment’s results also suggested that P. montanus did have an acute stress response when restrained. Future studies could replicate this research, but with a larger sample size and see if the results are congruent with the data obtained in this study.

Marine turtles are distributed in temperate, sub-tropical and tropical waters and beaches worldwide, often in areas heavily impacted by humans. Although there are many threats to marine turtle populations, the growing threats of nutrient pollution and harmful algal blooms are relatively understudied despite their widespread impacts on coastal marine ecosystems that marine turtles depend on. By studying juvenile green turtles (Chelonia mydas) in the Indian River Lagoon, Florida, where nutrient pollution and HABs are a widespread and longstanding issue, I aimed to conduct a case study of how these threats may affect this federally Threatened species. In Chapter 2, I used four concurrent, 18-year data sets to characterize and assess the interrelatedness of long-term trends in seagrass cover, macroalgae occurrence, juvenile green turtle abundance, and juvenile green turtle growth rates. From 2000 to 2018, IRL seagrass cover declined precipitously, macroalgae rose slowly through 2011 then declined during two severe HABs, juvenile green turtle abundance declined slowly, and growth rates declined through 2011 then rose through 2018. In Chapter 3, I conducted a 9-year study of juvenile green turtle foraging ecology using a comparative stable isotope approach. I found that carbon and nitrogen stable isotopic variance declined during and after two severe HABs in the IRL. In Chapter 4, I used two complementary methods to assess the diet of juvenile green turtles after two severe algal blooms in order to assess changes compared to previous diet studies. Visual identification of forage items showed that juvenile green turtle diet remained dominated by nutrient-tolerant red macroalgae with smaller components of seagrass and green algae; metabarcoding techniques largely failed to resolve their diet. My results highlight the web of complex effects and responses that factor in to determining the effects of nutrient pollution and HABs on juvenile green turtles. Future studies of habitat selection, foraging ecology, and the effects of these on juvenile green turtle growth and survival are needed to fully assess the threat of nutrient pollution.