<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> 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> 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> Gamefish populations in North America are experiencing increasingly elevated recreational fishing pressures; however, the impacts of current fishing regulations have not been evaluated for most marine species. Mandatory catch and release often results from size and bag limits with the assumption of fish survival and recovery with minimal sublethal effects. Depending on the intensity and duration of the stressor, acute stress from angling and handling can have deleterious physiological and behavioral impacts with consequences for fish health and fitness. We evaluated the short-term sublethal effects of angling-related stressors on kelp bass, <i>Paralabrax clathratus</i>, one of the most popular gamefish in southern California. Collaborating with recreational anglers to capture fish using standard hook and line practices, we evaluated biochemical responses and recovery by collecting blood samples at different time points after capture (10-120 min), after fish were released and some were recaptured (3h to 186 d). Blood cortisol, glucose, and lactate were significantly elevated and steadily increased in the hour following capture and holding (p &lt; 0.001). Fish caught, released, and recaptured after varying time at liberty were found to have returned to basal levels in &lt; 24 h (p > 0.05). Physiological stress responses were positively correlated with angling and handling duration, but negatively correlated with increasing fish size (p &lt; 0.05), suggesting that larger individuals may be more resilient to capture stress. Likewise, kelp bass exhibited no signs of cumulative or chronic stress from repetitive angling/recapture events and recovered to basal levels in &lt;24 h (p > 0.05). Kelp bass were also tagged with acoustic accelerometer transmitters and tracked to evaluate fine-scale behavioral effects of angling stress on their normal diel movement and activity. Reduced frequency of high acceleration movements (i.e. rapid feeding strikes) was observed for 33 h post-release, followed by recovery and evidence of elevated feeding behavioral activity. Rate of movement and area use size showed high individual and temporal variation; however, reduced movement immediately after release steady increased to normal levels over the first 10 h post-release. There was no discernable effect of angling on area use size, but areas of high relief substratum may be important refuge habitat for angled kelp bass during recovery. By integrating physiological and behavioral endpoints for kelp bass to standard angling induced stress we conclude that this species is able to recover in &lt;24 h; however, smaller individuals may be more susceptible to predation during this recovery period. Based on these findings, it is likely that kelp bass may still fair well under current size and bag limits.</p><p>