<p> The Magnuson-Stevens Fishery Conservation and Management Act (MSA; Magnuson-Stevens Fishery Conservation and Management Act. 2014. (16 U.S.C. 1801&ndash;1891(d)) mandates that fisheries management councils in the United States prevent adverse, or &ldquo;more than minimal and not temporary&rdquo;, fishing effects to essential fish habitat (EFH) to the extent practicable. Councils were left to decide what effects qualified as &ldquo;minimal&rdquo; and &ldquo;temporary&rdquo;. The lack of explicit definition in the MSA and its accompanying Final Rule has resulted in inconsistent habitat management throughout the country. The EFH mandate was written under an implicit assumption that councils have the scientific information necessary to effectively manage EFH. Basic information is lacking, such as what type of habitat occurs where, and how fishing effects habitat features. Chapter 1 briefly reviews the history of EFH regulation, the consequences of regulatory ambiguities and information gaps, and highlights that high latitude fisheries management can be disproportionately affected by climate variability. Thus, requiring investment in baseline habitat assessment and monitoring and renewed focus on under developed areas of research e.g. Fishing effects and gear-habitat interactions. </p><p> Councils have attempting to quantitatively describe fishing effects to EFH through the use of mathematical models. The most recent of which, the Fishing Effects (FE) Model, was used in the North Pacific Fisheries Management Council 2015 EFH Review cycle. The FE Model uses discrete time steps (monthly) and spatially explicit fishing effort and sediment data to calculate an estimated habitat disturbance. The FE Model is calculated in two-dimensions and implicitly assumes that if fishing gear does not contact the seabed, then there is no gear-habitat interaction. Some features stand taller than raised gear (e.g. sea whips, <i>Halipteris willemoesi</i>, in the North Pacific can up to 2m tall) and may interact with fishing gear. The FE Model in two-dimensions does not account for this potential interaction and cannot effectively simulate gear modifications. Chapter 2 proposes an adapted version of the FE Model that accounts for the vertical interactions through the use of discrete height bins. To accurately estimate interactions on and above the seabed, fishing gear has to be recharacterized. To demonstrate this the Bering Sea flatfish trawl was recharacterized by calculating how much of the nominal gear width is present in each height bin. A detailed methodology is provided to allow this method to be applied to any fishing gear. The adapted FE Model can be used to simulate gear modifications, as is shown by simulating two modifications of the flatfish trawl. This chapter will inform the 2020 EFH Review cycle as the FE Model is improved. </p><p>

<p> The domestication of tuna species has proven to be one of the most challenging endeavours in aquaculture. Among the issues yet unresolved is the occurrence of &lsquo;puffy snout syndrome,&rsquo; a condition in which tumour-like growths form on the head. Ultimately, vision and feeding are impaired and long-term afflictions typically result in mortality. Though few mentions of puffy snout exist in the literature, evidence suggests that it is not uncommon among facilities that hold tunas in captivity. The specific aims of this study were to: a) describe pathological features of puffy snout, and b) investigate its etiology through the evaluation of conditions and protocols at facilities rearing/holding tuna. </p><p> To describe pathological features of puffy snout, clinical signs were detailed by observing captive tunas in a land-based holding system, and examination of evidence of infection by parasites, bacteria, and viral agents was conducted on tissues collected from fish with and without puffy snout. Histological examination of tissue from normal and affected fish was also conducted. To investigate etiology, a survey was developed and sent electronically to 28 tuna-holding facilities globally. The survey inquired about the prevalence of puffy snout and the husbandry conditions and protocols employed (e.g., biological characteristics, capture and transport procedures, holding system design and water quality, feeding regime). These data were compared across facilities in an attempt to couple puffy snout prevalence with holding conditions and/or protocols. </p><p> Clinical signs of puffy snout included occlusion of the eyes and mouth, followed by changes to swimming and feeding behaviours. Parasitology, bacteriology, and virology examination all indicated no commonly-found pathological agents were responsible for inducing the condition. Histology showed that puffy snout is largely characterised by the apparent degeneration of muscle tissue with the replacement of a loose collagenous fibrosis and an undetermined fluid filling the interstitial space in tissues anterior to the eye. In dorsal musculature, collagenous growth may occur in the epidermal or hypodermal regions. </p><p> Based on survey data, the capture and transport process and feeding regime were unrelated to development of puffy snout. However, certain biological (e.g., fish size) and holding system (e.g., tank/pen size) parameters showed weak but non-dismissible coupling with puffy snout prevalence. Survey data and additional personal communication with field researchers confirmed that puffy snout in tuna is solely a captivity-related condition.</p>

<p> The introduction of lake trout <i>Salvelinus namaycush</i> into Yellowstone Lake preceded the collapse of the native Yellowstone cutthroat trout <i>Oncorhynchus clarkii bouvieri</i> population. As a system with a simple fish assemblage and several long-term data sets, Yellowstone Lake provided a unique opportunity to evaluate the ecology of a native salmonid in the presence of a non-native salmonid population undergoing suppression in a large natural lake. Diet data for Yellowstone cutthroat trout and lake trout were evaluated at varying densities to determine the effects of density on diet composition. Temporal diet shifts from 1996-1999 to 2011-2013 were likely caused by limitation of prey fish for lake trout. Diets, stable isotopes, and depth-related patterns in CPUE indicated lake trout > 300 mm consumed primarily amphipods, making them trophically similar to Yellowstone cutthroat trout from during 2011-2013. A lake trout removal program was initiated during 1995 to reduce predation on Yellowstone cutthroat trout. Abundance and fishing mortality were estimated for lake trout from 1998 through 2013 and Yellowstone cutthroat trout from 1986 through 2013. Density-dependence was evaluated by examining individual growth, weight, maturity, and pre-recruit survival as a function of abundance. In addition, a simulation model was developed for the lake trout-Yellowstone cutthroat trout system to determine the probability of Yellowstone cutthroat trout abundance persisting at performance metrics given potential reductions in lake trout abundance. Estimates of Yellowstone cutthroat trout abundance varied 5-fold and lake trout abundance varied 6-fold. Yellowstone cutthroat trout weight and pre-recruit survival decreased with increasing Yellowstone cutthroat trout abundance; however, individual growth and maturity were not related to abundance. Lake trout population metrics did not vary with lake trout abundance. Simulation model results were variable because of uncertainty in lake trout pre-recruit survival. Conservative estimates for required lake trout reductions were > 97% of 2013 abundance for a > 70% probability of Yellowstone cutthroat trout persistence at the performance metrics outlined in the Native Fish Conservation Plan. Lake trout removal will likely reduce lake trout abundance and result in Yellowstone cutthroat trout recovery if the amount of fishing effort exerted in 2013 is maintained for at least 15 years.</p>

<p> The South Texas Banks are a mesophotic coral ecosystem (30-150m deep). Understanding the community structure, biodiversity and, geographic connectivity of the South Texas Banks is essential with increasing threats from climate change, ocean acidification, invasive species, and pollution. In this study, a remotely operated vehicle (ROV) was used to examine the fish communities at five of the South Texas Banks: Big Adam, Hospital, Mysterious, North Hospital, and Southern. Reef fish were identified to the lowest possible taxon and enumerated from ROV transect video footage. A total of 3,838 demersal and pelagic fishes were recorded representing 61 species in 22 families including invasive <i>Pterois volitans. Bodianus pulchellus, Holocentrus adscensionis, Priacanthus arenatus,</i> and the Gobiidae family were the only fishes observed at all five banks. Habitat suitability models were created that highlight the rich biodiversity found on the South Texas Bank, which will warrant for future research and conservation efforts.</p>

<p> The impacts of a 20,993 L diesel and gasoline spill on the benthic macroinvertebrate (BMI) and diatom communities in Cold Creek and the Santa Ana River (below its confluence with Cold Creek) were assessed by comparing species richness, diversity and compositions between fuel-impacted and reference sites. BMIs and diatoms were sampled four times (13&ndash;26 months after the spill) in sites located upstream from the spill (reference) and in sites located 0.5, 1.3, 2.7 and 3.0 km downstream from the spill (impact). BMI communities up to 2.7 km below the spill and in Cold Creek had (1) lower species richness and diversity for at least 25 months after the spill and (2) dissimilar species compositions for up to 26 months after the spill when compared to the reference site. Diatom communities up to 2.7 km below the spill and in Cold Creek had (1) similar or higher species richness and diversity when compared to the reference site and (2) dissimilar species compositions when compared to the reference site for the entirety of the study. BMI and diatom communities located 3.0 km below the spill and in the Santa Ana River had similar species richness, diversity and compositions when compared to the reference site. These results provide evidence that the fuel spill had an impact on the BMI and diatom communities in Cold Creek and that these communities are still changing.</p>

<p> Though land conversion and flow alteration have heavily impacted the Sacramento River riparian ecosystem, restoration opportunities still exist in the hydrogeomorphically active Middle Reach. This study of riparian forest succession focused on six dominant riparian tree species to explore relative establishment timing and the potential impacts of altered flow regimes. We utilized tree inventory data and increment cores collected from riparian forest stands to establish a temporal chronosequence of floodplain surfaces and associated tree ages and colonization timing. Tree age calculations incorporated raw ring counts and sampling error simulations. Results were then used to construct species-specific, diameterage models and predict age distributions for all inventoried trees. Cottonwood&rsquo;s colonization window was longer than expected (up to 95 years after floodplain creation), whereas box elder and walnuts established on floodplains &lt;50 years old. This study lays the groundwork for future research into the health and development of the Middle Reach riparian forest.</p>

<p> Information on the movement of migratory demersal fishes such as Pacific halibut, Pacific cod, and sablefish is needed for management of these valuable fisheries in Alaska, yet available methods such as conventional tagging are too coarse to provide detailed information on migration characteristics. In this dissertation, I present methods for characterizing seasonal and annual demersal fish movement at multiple scales in space and time using electronic archival and acoustic tags. In Chapter 1, acoustic telemetry and the Net Squared Displacement statistic were used to identify and characterize small-scale movement of adult female Pacific halibut during summer foraging in a Marine Protected Area (MPA). The dominant movement pattern was home range behavior at spatial scales of less than 1 km, but a more dispersive behavioral state was also observed. In Chapter 2, Pop-up Satellite Archival Tags (PSATs) and acoustic tags were deployed on adult female Pacific halibut to determine annual movement patterns relative to MPA boundaries. Based on observations of summer home range behavior, high rates of year-round MPA residency, migration timing that largely coincided with winter commercial fisheries closures, and the demonstrated ability of migratory fish to return to previously occupied summer foraging areas, the MPA is likely to be effective for protecting both resident and migrant Pacific halibut brood stock year-round. In Chapter 3, I adapted a Hidden Markov Model (HMM) originally developed for geolocation of Atlantic cod in the North Sea for use on demersal fishes in Alaska, where maximum daily depth is the most informative and reliable geolocation variable. Because depth is considerably more heterogeneous in many regions of Alaska compared to the North Sea, I used simulated trajectories to determine that the degree of bathymetry heterogeneity affected model performance for different combinations of likelihood specification methods and model grid sizes. In Chapter 4, I added a new geolocation variable, geomagnetic data, to the HMM in a small-scale case study. The results suggest that the addition of geomagnetic data could increase model performance over depth alone, but more research is needed to continue validation of the method over larger areas in Alaska. In general, the HMM is a flexible tool for characterizing movement at multiple spatial scales and its use is likely to enrich our knowledge about migratory demersal fish movement in Alaska. The methods developed in this dissertation can provide valuable insights into demersal fish spatial dynamics that will benefit fisheries management activities such as stock delineation, stock assessment, and design of space-time closures. </p><p>

<p> Natural and sexual selection shape animal communication signals according to the demands of social context and the environment, which results in enormous variation in signal properties. My dissertation uses the electrocommunication signals of South American weakly electric knifefish to compare signal structure across several closely related species, with particular emphasis on signals that are extreme or unusual. Weakly electric fish continuously generate an electric field using an electric organ discharge (EOD). During short-range social interactions, fish produce chirps by rapidly and transiently increasing EOD frequency. I used recordings with playbacks of conspecific signals and hormone manipulation to characterize the sexually dimorphic chirp duration of <i>Parapteronotus hasemani</i>, a species of electric fish with high-frequency, long-duration chirps and huge variation in male morphology. I also described signaling behavior in <i>Distocyclus conirostris </i>, a species of electric fish with a low-frequency EOD and an unusual asymmetrical behavioral response to &ldquo;jamming&rdquo; created when EODs of similar frequencies interact. Next, I compared across species to examine how signal properties (EODs and chirping) interact to influence each other&rsquo;s detection and evolution. Certain signal parameters such as chirp frequency modulation and EOD frequency difference have substantial effects on chirp conspicuousness. Contrary to expectations, there was little support for a strict co-evolution in which a species&rsquo; chirps are most conspicuous on their own EOD waveforms. Thus, although EOD properties influence chirp conspicuousness, other factors such as the social or physical environment also likely shape chirp structure. Additionally, I show that EOD waveform may differ in perceptibility based on the EOD waveform complexity of the interacting fish. I consider how chirp conspicuousness could drive the evolution of sexually dimorphic chirps (such as those produced by <i>P. hasemani</i>), and I raise questions about whether low-frequency EODs (such as those produced by <i>D. conirostris</i>) contain sufficient information for fish to detect conspecific EOD frequencies using the neural mechanisms described in fish with high-frequency EODs. Taken together, these results show how the properties of multi-component signals shape each other and impact signal detectability. Finally, my dissertation concludes with a description of an innovative approach to teaching scientific communication skills in a highly structured undergraduate introductory biology lab.</p>

<p> Wetlands exhibit high primary productivity and play a significant role in the global carbon cycle. Brackish and salt marshes co-occur in Southern California; yet, restoration designs often eliminate remnant brackish marshes, along with their ecosystem functions, without evaluation. Vegetation, soil organic matter, and carbon flux were compared between brackish and salt marsh habitats in the Huntington Beach Wetlands. Newland Brackish Marsh had more carbon aboveground in denser and taller vegetation than the other two marshes. Brookhurst Salt Marsh sediments had more organic matter than the other two marshes. CH₄ emissions were negligible at all sites, and there were no differences in CO₂ flux or aerobic and anaerobic microbial respiration among sites. Although these components of the carbon cycle were similar among sites in this project, such quantitative functional evaluations should be part of the restoration planning process.</p>

<p>Estuarine organisms, such as juvenile penaeid shrimp, experience fluctuating oxygen pressures on a daily basis. In coastal waters of the southeastern United States, severe hypoxia (&lt; 4&ndash;6 kPa) is common in the summer, also a time during which bacterial concentrations in seawater are high. In response to invading bacteria, crustaceans mount an immune defense resulting in aggregations of circulating hemocytes. These aggregates can be trapped in and obstruct hemolymph flow through the gills, inhibiting oxygen uptake. Hypoxia itself is also known to inhibit immune function. In this study we investigated some key characteristics of penaeid shrimp that are likely to be associated with their ability to cope with hypoxia and bacterial infection. We compare critical Po₂, the oxygen pressure below which oxygen uptake depends on available ambient oxygen, in two commercially important shrimp species: wild <i> Litopenaeus setiferus</i>, the Atlantic white shrimp, and aquacultured <i> Litopenaeus vannamei</i>, the Pacific whiteleg shrimp. We also compare whole body lactate concentrations following acute exposure to severe environmental hypoxia (5.3 kPa), and injection with a sub-lethal dose of bacteria (<i> Vibrio campbellii</i> 90-69B3), in aquacultured <i>L. vannamei</i> and in wild-caught <i>Farfantepenaeus duorarum</i>, the Atlantic pink shrimp. LD₅₀ tests indicate that the virulence of <i> V. campbellii</i> in <i>L. setiferus</i> (LD₅₀ = 6.4 &times; 10⁵ CFU g^&minus;1 shrimp) is similar to that previously determined in <i>L. vannamei</i> (LD₅₀ = 3.06 &times; 10⁵ CFU g^&minus;1 shrimp). We found no difference between <i>L. vannamei</i> and <i>L. setiferus </i> in critical Po₂, which fell between 3.5&ndash;5.2 kPa in both species. Whole body lactate concentration was measured in shrimp held in normoxia (>16 kPa) or hypoxia and injected with saline or bacteria. There were no effects of exposure in <i>L. vannamei</i>, however lactate concentration in <i>F. duorarum</i> increased by 60% in shrimp exposed concurrently to hypoxia and injected-bacteria, compared to saline-injected shrimp exposed to hypoxia and <i>Vibrio</i>-injected shrimp exposed to normoxia. This is consistent with previous findings in our lab, that hemocyanin in <i>L. vannamei</i> has a higher concentration and O₂ affinity, resulting in better tissue oxygenation, than that in wild species of Atlantic shrimp. These data suggest that aquacultured <i>L. vannamei </i> has an adaptive advantage over at least one species of wild penaeid shrimp in coping with hypoxia and bacterial infection. </p>