Over the past few decades, there has been increased research focus on carbon cycling within aquatic systems, especially with the changing global climate. Inland waters play a major role in the global carbon cycle, but the fundamental features remain poorly understood, particularly the large lakes of the world. Our experimental approach assessing the carbon budget of Lake Superior, the largest freshwater lake by area, provides spatial and temporal variability that has been previously overlooked but may be critical to our understanding on the biogeochemical processes controlling the lake. Multiple stations were chosen across the lake, both nearshore and offshore, to evaluate the variability in physical mixing regimes and biogeochemical processing. Short and long-term carbon consumption measurements were coupled to assess the heterotrophic activity relative to the lability of dissolved organic carbon. Partial pressure of carbon dioxide (pCO2) was directly measured to determine the metabolic nature of the lake and the amount of carbon dioxide (CO2) that fluxes across the air-water interface. The pCO2 results were further coupled with an isotopic approach measuring oxygen-18 (δ18O) to evaluate how the metabolism of Lake Superior has changed over a decadal scale. A range of environmental factors, including temperature, photodegradation and source/quality of organic carbon, influenced short and long-term carbon consumption. In-situ pCO2 observations supported a temporal switch in metabolism from the lake being a source of CO2 in the spring to being a sink in the summer driven by biological components of the system. When the pCO2 results were coupled with the isotopic measurements over the past decade (1999-2011), Lake Superior was dominated by respiration during isothermal conditions and production during stratification. In the past decade, Lake Superior has experienced increased surface water temperatures, shifting the metabolic state to a shorter net heterotrophic period in the spring and a longer net autotrophic period in the summer. This research highlights fundamental aspects of Lake Superior’s metabolism that have been previously understudied, as well as providing key information about processes controlling its carbon budget, and giving a better understanding of how climate change will continue to impact Lake Superior.

Wildlife in captivity has a long history of benefiting global conservation goals. Captive animals can raise awareness and appreciation for the conservation of endangered species. Additionally, captive animals can be used as source populations to reintroduce animals back to the wild or to supplement existing wild populations. The rapid increase in amphibian species threatened with imminent extinction has necessitated the creation of dozens of captive-breeding programs. The focus of this dissertation has integrated topics across the spectrum of animals in captivity and the wild, and the results provide useful recommendations for conservation action. First, I describe how market pressures over a 28-year period are causing meteoric increases in the prices of amphibians sold in the pet trade, indicating a high risk of overexploitation. Pet amphibians may facilitate greater understanding and appreciation of amphibians, but the pet trade must be sustainable. Improving amphibian husbandry will increase the number of captive-bred animals available in the pet trade, and it will allow greater production of threatened species for reintroductions. Secondly, by performing a systematic review of husbandry for 289 amphibian species native to the US, I identified a critical lack in taxon-specific husbandry and developed husbandry research prioritizations. Next, I used a combination of laboratory and field studies to examine domestication processes in amphibians by comparing defensive behaviors in two species of captive-bred and wild poison frog. Captive-bred amphibians had significantly reduced defensive behaviors compared to wild conspecifics, likely resulting from habitation processes related to their husbandry. Finally, I performed three reintroductions of the critically endangered Wyoming Toad (Anaxyrus baxteri) in Wyoming, US. I demonstrated how providing a transitionary period, called a soft-release, to captive-bred toads moving to a novel, wild environment can improve reintroduction success. My work illustrates how improving our understanding of the nexus between captivity and the wild can improve conservation action for endangered species.

The resilience of coral reefs depends, among others, upon local physical and biological characteristics. This dissertation focused on how herbivory, structural complexity, and sedimentation can impact the structure, function, and, ultimately, resilience of Caribbean coral reefs. We filled an important knowledge gap related to trophic niche and ecological roles of surgeonfishes (A. coeruleus and A. tractus), two of the most important herbivorous fishes in the Caribbean. We showed that both species feed primarily on turf algae preventing further progression of algal succession while A. tractus may also help reduce macroalgal abundance by targeting common macroalgal species such as Dictyota spp. We used a factorial experiment to analyze the interactive effects of herbivory (exclosure vs. open plots) and reef structural complexity (vertical vs. horizontal substrate orientation), on the development of benthic communities. We found that vertical substrates were quickly dominated by crustose algae regardless of herbivory treatment while succession of horizontal substrates was determined by herbivory. Our results suggest that at small scale, reef complexity is a major factor determining algal community structure. We investigated why, despite high levels of herbivory, coral cover in South Florida has failed to recover. We surveyed benthic composition, grazing and abiotic characteristics along six spur and groove reefs in the Florida Keys. Using boosted regression tree analyses, we found that sediment abundance was the best predictor of both juvenile and adult corals, which could explain the failure of coral recovery. We studied spatial and temporal changes of reef communities of reefs in Havana, Cuba where global and local stressors have affected coral communities while overfishing and nutrient enrichment has led to low herbivory levels. Our surveys revealed a region-wide high abundance of algae (~60%) as a consequence of heavy overfishing with likely negative consequences on coral recovery. In summary, my dissertation showed context-depend effects of herbivory, structural complexity, and sediment on Caribbean coral reefs. While reduction of herbivory can often suppress coral recovery, on coral reefs with robust herbivore populations, physical factors such as structural complexity and sediment may still limit coral recovery and fundamentally impact reef resilience.

Since the texture of surfaces plays a key role in the shaping of many environmental processes, high resolution measurements are important to study these phenomena. Specifically, 3-D point cloud data is desirable to document river shape and evolution, surface roughness, and erosion-sedimentation processes. The best method of obtaining these measurements is using a terrestrial laser scanner. However, these are too expensive for limited-use experiments. Therefore, I developed a simple, affordable, and robust system used to acquire high resolution data relating to hydraulic and fluvial environments.

Non-native invasive plant species can often have negative effects on native ecosystems, such as altered nutrient cycling, decreased habitat for wildlife, and outcompeting native plants. Around the Great Salt Lake (GSL), Utah, the invasive wetland grass Phragmites australis has become abundant in wetlands around the lake. Phragmites is replacing many native wetland plants provide important waterfowl habitat around the GSL. For successful management of Phragmites in GSL wetlands, it is important to know the current distribution of Phragmites, as well as areas that might be vulnerable to future invasion by Phragmites. To do this, we used multispectral aerial imagery to map the current distribution of Phragmites. We then created a model that statistically related the Phragmites distribution data to a suite of environmental predictor variables such as salinity, proximity to nutrient sources, or proximity to roads. Results from our model suggest that Phragmites is more likely to be found in wetland areas close to point sources of pollution, with lower elevations with prolonged inundation, and with moderate salinities. We used these results to identify areas around GSL that might be vulnerable to future invasion. Results from our study will assist wetlands managers in prioritizing areas for Phragmites monitoring and control by closely monitoring areas of prime Phragmites habitat.

Terrestrial auroras are visible-light events caused by charged particles trapped by the Earth's magnetic eld precipitating into the atmosphere along magnetic eld lines near the poles. Auroral events are very dynamic, changing rapidly in time and across large spatial scales. Better knowledge of the low of energy during an aurora will improve understanding of the heating processes in the atmosphere during geomagnetic and solar storms. The Auroral Spatial Structures Probe is a sounding rocket campaign to observe the middle-atmosphere plasma and electromagnetic environment during an auroral event with multipoint simultaneous measurements for fine temporal and spatial resolution. The auroral event in question occurred on January 28, 2015, with liftoff the rocket at 10:41:01 UTC. The goal of this thesis is to produce clear observations of the magnetic eld that may be used to model the current systems of the auroral event. To achieve this, the attitude of ASSP's 7 independent payloads must be estimated, and a new attitude determination method is attempted. The new solution uses nonlinear least-squares parameter estimation with a rigid-body dynamics simulation to determine attitude with an estimated accuracy of a few degrees. Observed magnetic eld perturbations found using the new attitude solution are presented, where structures of the perturbations are consistent with previous observations and electromagnetic theory.

Humans have indirectly and directly contributed to the extinction of over 500 species within the past 500 years, a rate far higher than we have seen in the past. The high extinction rate and the fact that 18% of vertebrates may become extinct within the next century have pushed Earth into a biodiversity crisis. Understanding what makes species more at risk of extinction is needed to protect Earth’s biodiversity. Generally, it is expected that predators have greater extinction risk than omnivores and herbivores because predators are larger in body size, depend on other animal species for food, need large home ranges, and have fewer individuals within their populations. However, no study to date has actually tested the assumption that predators have the highest extinction risk. This question is important to understand because diet is associated with the ecological role a species plays in an ecosystem. We compared the extinction risk of species with different diets to determine species in which trophic level are proportionately more at risk of extinction. We classified each species’ diet, trophic level (i.e.,predator, omnivore, and herbivore), body size, habitat, geographic region, system, and associated threats. We focused our analyses on all mammals, birds, and reptiles assessed by the International Union for the Conservation of Nature. We then compared the expected and observed proportions of threatened species within each trophic level and diet group at global, system, habitat, and regional scales. We found that predators, except scavengers, fish-eating birds, and obligate mammal and bird eaters, were not more threatened than expected. On the other hand, herbivores consistently had greater proportions of threatened species than expected. Specifically within herbivores, fruit, grass, and leaf-eating species had high proportions of threatened species. When we separated large-bodied and small-bodied species, we found that most large-bodied species, regardless of their trophic level, had greater proportions of threatened species. When we looked at the regions and habitats where species were more often threatened, we found that herbivores were highly threatened in south and Southeast Asia, sub-Saharan Africa, and Oceania. In addition, herbivores were highly threatened in tropical forests, marine coasts, and sometimes grasslands. Overall, terrestrial herbivores and marine predatory birds were highly threatened. We found that these patterns may have resulted from overexploitation, habitat alteration, and pollution targeting herbivores and sometimes omnivores. These findings suggest that we should shift conservation focus from predators to include herbivores. The most threatened species, tropical herbivores, scavengers, and mammal, bird, and fish eaters should be of highest conservation priority.

In 1993, to determine if wild-strain mallard releases could be used as a management practice to increase local mallard breeding populations, I released 2,344,4.5- week-old mallard ducklings (1,200 females and 1,144 males) to wetlands on 12,10.4-km2 sites (approximately 200 per site, 100 females, 100 males) in the North Dakota Prairie Pothole Region. I monitored the release sites to determine if any relationship existed between site characteristics and time of release to duckling survival estimates. I conducted breeding pair surveys during 1994 and 1995 on treatment and paired control sites to compare post-release population levels. Lastly, I analyzed return data and habitat use, and conducted behavioral experiments to determine if wild-strain mallards experienced higher mortality rates and if any observed differences could be explained by behavior. In 1994,1 observed 55 of the nasal saddled ducklings returning as adult fem ale to the release sites. In 1995, only 5 nasal saddled females were observed, both on treatment and control sites. No difference was observed hi breeding pair populations on treatment and control sites in 1994 (P = 0.18) and 1995 (P = 0.59). Hard-released wild-strain mallard females had lower survival rates than wild (P = 0.01) and modified gentle-release wild-strain females (P = 0.05). Ail wild-strain females were virtually eliminated from the population by year 4. This suggests that these buds may have been more vulnerable to predation and other mortality factors than wild females. Breeding wild and wild-strain mallard females reacted similarly to human approach, but when flushed, wild females flew farther than wild-strain females (P = 0.0002). Wetlands used by wild-strain females differed from wild females during breeding by type (P < 0.0001) and cover (P = 0.0003) classification. Wild-strain females selected larger, more permanent wetlands exhibiting less emergent vegetation than did wild counterparts. These differences may help to explain why wiki-strain mallard releases did not increase local breeding populations. The lack of band recoveries for wild-strain females during the latter years when viewed in the context of the observed behavioral differences suggests that these birds were unable to adapt to conditions in the wild.

Whitefish populations around the world have long been difficult to categorize taxonomically. The whitefish of Bear Lake, Utah/Idaho are no exception. There are three recognized species of Prosopium that are endemic to the lake. Two of these species, Prosopium spilonotus and Prosopium abyssicota, have previously been indistinguishable outside of spawning times. Previous studies have proposed additional taxa within P. spi/onotus to further complicate the identification among these taxa. Morphological characteristics were quantified on wild whitefish from Bear Lake, as well as from progeny reared in the laboratory from the wild adult fish. The purported taxa were separated in the field using the best characteristics presented in previous studies, and the progeny were reared separately in these groups. Otolith aging was also done on the wild adult fish to understand the age structure of the spawning populations. Results from otolith aging and morphological analyses on the laboratoryreared fish indicated that there is only one taxonomic group of P. spilonotus. By using scale counts, it was determined that P. spilonotus and P. abyssicola can be distinguished from each other with considerable reliability.

Accurate fishery-independent methods for assessing the abundance of marine fish stocks are important tools for proper pelagic fisheries management. The review and improvement of standardized sampling methods used in fisheries-independent sampling, and the establishment of improved models of abundance and population dynamics utilizing novel statistical techniques for fisheries management will further improve our understanding of the way in which marine fish stocks vary spatially and temporally. One of the most important and longest running surveys of fisheries-independent data in the Southeastern United States is the spring ichthyoplankton survey conducted through the Southeast Area Mapping and Assessment Program (SEAMAP). These surveys of highly migratory pelagic fish larvae and eggs in the exclusive economic zone of the USA in the Gulf of Mexico have been conducted annually during spring spawning periods (March to June) since 1982 by the National Oceanic and Atmospheric Administration (NOAA) National Marine Fisheries Service (NMFS). A primary focus of this survey is collecting the data used in a larval abundance index of bluefin tuna (Thunnus thynnus) for "tuning" population estimates for the western Atlantic stock of this species using virtual population analysis (VPA). As with many other forms of fishery independent data, there is statistical overdispersion of larval fish and high variability in catch rates related to non-static environmental conditions. This variability in catch rates, along with zero-inflated estimates of abundance, i.e. characterized by high numbers of stations with low or zero catches, present problems in deriving accurate and reliable stock assessments for western Atlantic bluefin tuna. The research presented here was conducted in an effort to improve the decision support system used in managing bluefin tuna in the western Atlantic, by improving catch rates of their larvae during spring ichthyoplankton cruises. A major focus of which was to overcome challenges related to reducing the variance of the larval index of abundance. The research presented here, explored the influence of sampling design and oceanographic conditions on an assemblage of commercially important taxa within the Gulf of Mexico. Such studies are necessary to evaluate differences in habitat utilization within a specific complex or among assemblages of closely related taxa. The spatial and temporal patterns of larval bluefin tuna (Thunnus thynnus) were analyzed in relation to mesoscale patterns of circulation, types of sampling gear used during fishery independent surveys, and in the context of common oceanographic variables associated with the spawning habitat of this iconic pelagic predator. Collaterally the relationship between the above factors on spatial and temporal patterns of the larvae of seven congeneric species of marine fish, whose larvae commonly occur with bluefin tuna, during the spring spawning season in the Gulf of Mexico (Auxis spp., Euthynnus alleteratus Corphaena spp., Katsuwonus pelamis, other Thunnus spp.: Thunnus albacares and Thunnus atlanticus, Istiophoridae, and Xiphias gladius) was investigated. The historical distribution of abundance in these eight taxa of larval epipelagic fish were analyzed in the context of mesoscale and large scale circulation features in the Gulf of Mexico between 1994 and 2008. Characterization of these features was conducted using concurrent, synoptic satellite altimeter, sea surface temperature (SST), and ocean color (OC) observations. Larval abundance among mesocale features was examined for the eight pelagic fish taxa using permutational multivariate analysis of variance (PERMANOVA). All but one taxon, T. thynnus, showed differences in occurrence across features. Additionally only two taxa (X. gladius and Istiophoridae) did not show highest abundances in "Common Waters" of the Gulf of Mexico. The abundance of the eight taxa, when examined in aggregate or as an assemblage, differed significantly between circulation features. However, distributions of individual taxa among circulation features differed for only the other Thunnus spp. taxa, which incorporates Thunnus albacares and atlanticus. The results from this study indicated that for most of the individual taxa studied, and Thunnus thynnus in particular the distribution of spawning habitat in the Gulf of Mexico is not associated with specific patterns in circulation. To analyze the impact of sampling gear on larval epipelagic abundance, the collection methods of the eight taxa during spring surveys, including a new net sampling methodology tested in surveys between 2009 and 2011, were compared. This new sampling methodology consisted of a 1x2 m frame fitted with a 0.505 mm mesh net, towed in a yo-yo fashion between the surface and 10m depth, referred to as the S-10 net. Sampling effectiveness between gears was compared by examining the abundance and length of the eight taxa of larval fish. A PERMANOVA of net type and time of sampling (day/night) on abundance and mean body length (BL) indicated that net type was a significant factor in assessing abundance and BL for all taxa. Highest mean assemblage and individual taxa abundance for seven of the eight taxa were in S-10 samples. Depth discrete sampling of the upper 50 m indicated that highest abundances for all scombrid taxa were found in the upper 30 m and provided justification for the improved sampling efficiency of the S-10 net. These results indicate that distributions of these epipelagic fish are not truly neustonic and that sampling effectiveness for them strongly depends on depth range fished by the net. Finally, the results of two research cruises using the new sampling methodology (S-10 net) during the spring of 2010 and 2011 were investigated to explore larval fish assemblages. Canonical analysis of principal coordinates (CAP) was used to evaluate the horizontal distribution of eight taxa of epipelagic larval fish and to relate these distributions to a total of eight variables observed through in-situ and remotely obtained data. Larval assemblages were established for the CAP via unweighted pair group method with arithmetic mean (UPGMA) hierarchical clustering utilizing similarity profile analysis (SIMPROF) tests for stopping rules. Further refinement to five common assemblage groups was obtained using indicator species values (INDVALS) and percent composition of taxa abundance within groups. Total model accuracy was 54%, with highest classification success for the assemblage group characterized by T. thynnus and the other Thunnus spp. (64%), and lowest classification success for negative stations (22%). Changes in the assemblage of these larval fish were partially explained by the seasonal progression in day-length, and related changes in sea surface temperature. Depth, chlorophyll a concentration, salinity, and optical clarity were also important. Five assemblages of larval fish were identified, characterized by differences in the relative abundance of the five taxa of scombrids, and the Coryphaena spp. taxa, and indicated a high degree of shared spawning habitat. The differences in habitat utilization by these taxa is highly influenced by seasonal changes in sea surface temperature, and large scale differences in depth and water masses in the Gulf of Mexico. This results in a gradual shift from groups with smaller and more abundant coastally influenced taxa with protracted spawning seasons to the larger sub-tropical, more pelagic species across a large expanse of shared spawning habitat. This dissertation research provides a context to the historical assessment of abundance, evidence for the association of specific taxa with particular oceanographic conditions, and improved assessment capabilities for epipelagic larval fish. As this research shows the spawning habitat of these taxa in the Gulf of Mexico are largely shared, and the influence of environmental variables only partly addressed the spatial and temporal variance attributed to larval abundance in the Gulf of Mexico. The improved methods used in this study will be useful to researchers studying the factors impacting larval recruitment and survival of highly migratory species, and comprehensive ecosystem based resource management. The results will improve fisheries-independent sampling and management for highly migratory species, and provides new methods for evaluating larval fish assemblages within the framework of oceanographic conditions for large marine ecosystems.