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<p> As a result of human activities, the level of CO₂ in the Earth&rsquo;s atmosphere has increased by nearly 40% since the industrial revolution. The rate of green house gas emission is accelerating, with current trends exceeding those predicted by &ldquo;worst case&rdquo; global climate change scenarios. The chemistry of the ocean is fundamentally changing as a result of increasing atmospheric CO₂, which dissolves in seawater, making it more acidic, a process referred to as ocean acidification (OA). A rapidly expanding body of science is now being generated to understand the impact of this global environmental change. To date, most studies evaluating OA effects have centered on simplified laboratory analyses that expose single populations to short-term treatments in order to quantify responses of individuals. These designs offer a limited assessment of the degree to which phenotypic plasticity and local adaptation might influence the response of populations to OA. </p><p> To address these questions, I carried out studies on members of Phylum Bryozoa, a species-rich clade of calcified colonial marine invertebrates distributed throughout the global ocean. Bryozoans were selected as a model system for this work because the clade exhibits a broad array of growth and calcification strategies, and because of the relative paucity of data regarding their expected response to future acidification. In addition, bryozoans can be subdivided into genetically identical replicate clones, which can then be assigned to separate treatments, allowing variation across treatments to be uniquely partitioned into the variance components of statistical models. In order to culture bryozoans for comparative experiments, I designed and constructed a new flow-through OA system at the Bodega Marine Laboratory, capable of finely manipulating both the temperature and carbonate chemistry of seawater, allowing for controlled laboratory experiments of long duration. </p><p> In Chapter 1, I performed a comparative 9-month laboratory experiment examining the effects of ocean acidification on the native Californian bryozoan <i> Celleporella cornuta. C. cornuta</i> was sampled from two regions of coastline that experience different oceanographic conditions associated with variation in the intensity of coastal upwelling. Under different CO₂ treatments, the biology of this bryozoan was observed to be remarkably plastic. Colonies raised under high CO₂ grew more quickly, invested less in reproduction, and produced skeletons that were lighter compared to genetically identical clones raised under current atmospheric values. Bryozoans held in high CO₂ conditions reduced their investment in skeletal carbonate, changed the Mg/Ca ratio of skeletal walls and increased the expression of organic coverings that may serve a protective function. Differences between populations in growth, reproductive investment, and the frequency of organic covering production were consistent with adaptive responses to persistent variation in local oceanographic conditions. </p><p> In Chapter 2, I tested whether skeletal mineralogy can vary plastically in some invertebrates using the cosmopolitan bryozoan <i>Membranipora tuberculata</i> as a model. In a 6-month laboratory experiment, I cultured genetic clones of <i>M. tuberculata</i> under a factorial design with varying food availability, temperature, and dissolved CO₂ concentrations. Elevated food availability increased growth in colonies while cold temperatures and high CO₂ induced degeneration of colony zooids. However, colonies were able to maintain equivalent growth efficiencies under cold, high CO₂ conditions, suggesting a compensatory tradeoff whereby colonies increase the degeneration of older zooids under adverse conditions, redirecting this energy to the maintenance of growth. Elevated food and cold temperatures also decreased Mg concentrations in skeletal material, and this skeletal material dissolved less readily under high CO₂ conditions. This suggests that these factors interact synergistically to affect dissolution potential in this and other species. </p><p> Finally, in Chapter 3, I explore stable isotope values for &delta;¹⁸O and &delta;¹³C in the calcium carbonate structures of the bryozoan <i>Membranipora tuberculata</i>. I tested whether this species accurately records both temperature and pH variability during periods of coastal upwelling by analyzing &delta;¹⁸O and &delta;¹³C in colonies grown in the field and in controlled laboratory cultures. Field-grown colonies were out planted next to a Durafet^&reg; pH sensor, which provided a high-resolution record of the temperature and pH conditions these colonies experienced. &delta;¹³C was found to negatively co-vary with pH in both laboratory and field growth, and calculated field temperatures derived from laboratory &delta;¹⁸O temperature calibrations aligned with the records from the pH sensor. &delta;¹⁸O_c values were more depleted under low pH in laboratory trials, which stands in contrast to patterns observed in other taxa. This may indicate that <i>Membranipora</i> utilizes bicarbonate ion (HCO₃^-) in its calcification pathway, and could help explain why many bryozoan species appear to exhibit enhanced growth under high CO₂ conditions. (Abstract shortened by ProQuest.)</p>

<p> Marine Protected Areas (MPA) are broadly used to protect marine ecosystems, restore biomass, and increasingly as tools in fisheries management for benthic stocks. Nevertheless, MPAs are seldom used to target pelagic species due the challenges of designing an effective MPA in a highly dynamic environment. It is believed that highly mobile organisms will get few benefits, since they leave the protected area too frequently. One possible solution is to compensate for such movement with larger MPAs. Nevertheless, uncertainty about the benefits in the face of vagaries about fish movement make it unlikely that such efforts would be successfully pursued. </p><p> Although it is a generally accepted that MPAs provide multiple benefits if well designed, empirical demonstrations of benefits from MPA are hard to obtain. They require long term evaluations, and as a consequence, comparisons between alternative MPA designs are almost nonexistent. Simulation models provide an alternative to empirical approaches that allow tests of designs and forecasts of potential outcomes. To date, most of the simulation models of MPAs have been developed for benthic systems, where simplified assumptions about fish and fisherman movement are reasonable. Fortunately, with the advent of more realistic fish movement models, new approaches are now possible that can combine complex individual-based models of movement, population dynamics and virtual MPA systems. The use of these new complex simulation models can guide the optimization of MPA design to increase both stock sizes and fisheries yields. </p><p> The goal of the research presented in this dissertation is to study the potential of a large MPA to protect a pelagic stock and determine how fish movement characteristics and complex environmental dynamics influence the optimal design criteria for a successful pelagic MPA. The findings are timely given increasing interest in developing large no fishing zones to protect overfished pelagic stocks, especially for those taxa whose distribution spans more than one exclusive economic zone or resides in international waters. For this purpose I implemented a simulation model that incorporates detailed fish movement and their responses to complex environmental forcing to study the effect of fish movement on the efficacy of MPAs of different size and location. (Abstract shortened by ProQuest.)</p>

<p> As eel populations decline worldwide, research tools for scientists and managers to better understand eel populations and dynamics will be vitally important. This research focuses on the relatively understudied silver phase eel, the sexually mature adult life stage that will make the single spawning journey to the oceanic spawning grounds. A non-lethal index of eel maturity was designed based on external measurements and was able to correctly classify individuals into one of seven maturity classes 83% of the time overall, yielding similar results to other non-lethal indices. Habitats above and below barriers to migration, at varying levels of watershed urbanization, and different distances from the ocean were compared in terms of eel maturity, size, age, and parasite parameters. Two methods of bioelectrical impedance analysis (BIA) were evaluated in their ability to estimate eel lipid concentration, a key factor in eel maturity and successful spawning.</p>

<p> Streams along the Copper River Delta, southcentral Alaska, exhibit contrasting thermal and hydrologic variability associated with being primarily groundwater-fed (GWF) or surface water-fed (SWF). Groundwater-fed streams are predictable both thermally and hydrologically year round, whereas SWF streams are unpredictable and exhibit more variable thermal and hydrologic regimes. These differences may strongly influence aquatic insect community structure and secondary production. Four streams, two GWF and two SWF, were sampled twice monthly from late April 2013 through August 2013 and once seasonally in fall (September) and early winter (November). Aquatic insect community structure differed markedly in both hydrologic types. Taxa richness was significantly higher in SWF (43) than in GWF (39) streams and non-metric multidimensional scaling of community structure revealed two distinct groups corresponding to the two hydrologic types. Total secondary production was higher in GWF than in SWF streams with Orthocladiinae (Diptera: Chironomidae) representing 56% of insect secondary production in GWF streams. Results from this study have strong implications for aquatic insect communities in GWF and SWF streams because of differing susceptibilities of these systems to the potential effects of climate change. Due to their thermal stability, groundwater-fed streams are less likely to be impacted by climate change, whereas SWF streams are thermally variable and more likely to be influenced. The effects of altered aquatic insect communities can cascade to higher trophic levels such as salmon and ultimately impact stream ecosystem function and the ecosystem services they provide.</p>

<p> Government agencies assess the biological integrity of streams and the chemistry of groundwater to monitor anthropogenic impacts on freshwater ecosystems. Some of the impacted streams lack obvious stressors that can be linked to the impacts. In the case of elevated nutrients and ionic concentrations found in impacted stream sites within the Malibu Creek Watershed, research from the Las Virgenes Municipal Water District pointed towards the naturally occurring leachate from the Modelo formation, which contests previous studies suggesting an influence from anthropogenic activity. Differentiating between natural sources of trace element concentrations and point/non-point source contamination could aid in resolving water quality issues since monitoring occurs near anthropogenic development. Water, bedrock, and diatoms were sampled from spring, seep, and stream sites underlain by Tertiary sedimentary bedrock throughout the study area. Multivariate analyses revealed an association of groups driven by salinity along with a correlation between geochemistry and diatom assemblages. Mixing models and radar charts identified potential rock types as sources for analyte concentrations. Sites that were underlain by the Modelo formation presented brackish water conditions and high nutrient concentrations, which potentially influenced the diatom species compositions found at the spring/seep sites as a result of weathering.</p>

<p> Eulachon smelt <i>Thaleichthys pacificus</i> are anadromous forage fish of the North Pacific Ocean that annually spawn in coastal rivers of North America in late winter and early spring. These spawning runs range from northern California to southwestern Alaska and provide important resources to nearby communities, indigenous cultures, and wildlife predators. However, eulachon life history is not well understood or documented throughout their range. In recent years, concerns for eulachon population abundances in the southern portions of their range have led to federal protection. Though there are no federal listings in Alaska, there have been local concerns documented for eulachon runs of the Chilkat and Chilkoot rivers since approximately 1990. However, eulachon run timing and abundance trends are difficult to detect due to limited available data and variability in eulachon runs. To document baseline information and explore patterns of eulachon runs of the Chilkat and Chilkoot rivers, we sought local and traditional knowledge from residents of nearby communities to document information about local uses, run timing, abundance, and wildlife observations related to eulachon runs. Observations of eulachon runs were integrated with historical records from newspaper articles and scientific reports to construct temporal trends in eulachon run timing and abundance. </p><p> Based on the findings of this study, annual eulachon runs of the Chilkat and Chilkoot rivers generally occur for about a week or two between mid-April and mid-May. The arrival dates of eulachon runs often vary from year to year, but the timing appears to have shifted earlier, from mid-May to mid-April, over the past couple of decades. Abundance records were not sufficient to quantify trends. However, qualitative information regarding abundance did not suggest any clear trends in eulachon abundances of the Chilkat and Chilkoot rivers over the years, nor did there appear to be prominent local concerns about abundance declines. Many respondents suggested that eulachon populations were naturally too variable to be able to describe trends in abundance. Interviews also provided insight into local perspectives on eulachon life history and ecology. These results suggest that variability in eulachon run timing and abundance could be related to environmental conditions, including tidal height, river habitat, and water temperature. For a data-limited species like eulachon, integrating local observations and historical records offers a promising approach to documenting baseline information and improving the scientific understanding of eulachon runs and other environmental phenomena.</p>

<p> An aquaculture production system was constructed at the Waik&imacr;k&imacr; Aquarium in the fall of 2016 that produces mysid shrimp zooplankton (<i> Americamysis bahia</i>). From November 2017 to February 2018, the Waik?k? Aquarium (WAq) required an average of 5,751 live mysids per week that were imported as feed with current import rates of $0.08 per animal or$24,000 annually. Fixed and variable budgets were used to evaluate the economics for the mysid culture system. Sensitivity analyses of labor costs, the sale of excess mysid production, and the discount rate were also conducted using stochastic modeling of in-house domestic yields to estimate the expected the net present values (NPV) of domestic production in comparison with imports. The indirect benefits of domestic production were qualitatively evaluated. Results showed that WAq had a greater (> 0) NPV across a variety of cost and benefit scenarios and a less expensive $.05 mysid versus the imported $.08 mysid.</p><p>

<p> Bighead Carp <i>Hypophthalmichthys nobilis</i> and Silver Carp <i> H. molitrix</i> (collectively referred to as bigheaded carp) were introduced to the United States in the 1970s and escaped into the Mississippi River from aquaculture ponds. Since their escape, bigheaded carp have become established in the Mississippi River Basin, including the Ohio River and its tributaries. More recently, bigheaded carp have invaded the Tennessee and Cumberland rivers. Little research has been conducted on bigheaded carp in Tennessee waters, with preliminary studies investigating the distribution and characteristics of established bigheaded carp populations, including growth rates and recruitment. My study represents the first systematic sampling of bigheaded carp in the Tennessee and Cumberland rivers, both tributaries to the Ohio River, and in large reservoirs in the southeast U. S. Standardized, multi-gear sampling methods were used to sample bigheaded carp in Kentucky Lake and Pickwick Lake on the Tennessee River and Lake Barkley and Cheatham Lake on the Cumberland River in 2017 and 2018. Overnight gill nets were the most effective gear, capturing an average of 17 Silver Carp per gill net gang. Short-set gill nets captured an average of one Silver Carp per gill net gang, and electrofishing captured an average of one Silver Carp per 10-minute electrofishing transect. Maximum total length (TL) was 1,390 mm for Bighead Carp and 1,111 mm for Silver Carp, and the maximum age for both species was 11 years. Average age and condition of Silver Carp was higher in upstream impoundments than downstream, and thus suggested an early invasion period from Ohio River movements. Gonadosomatic index (GSI; egg mass weight to body weight ratio) was also higher in upstream impoundments than downstream impoundments. Higher GSI values were observed in the spring and summer, when bigheaded carp may begin to spawn in response to high flows. Length-at-age estimates for the four reservoirs suggested bigheaded carp growth rates in the Tennessee and Cumberland rivers are similar to other populations in the US, indicating populations may be experiencing density effects in southeastern impoundments. No young of year (YOY) bigheaded carp were captured during the study, but weak and missing year classes due to erratic recruitment patterns are common in bigheaded carp, and monitoring for YOY fish should continue. Mean catch-per-unit-effort (CPUE) was not significantly different among reservoirs for the three gear types, and no significant seasonal variation in mean CPUE was observed for overnight gill nets. A lack of differences in CPUE across sampling seasons suggested population densities could be assessed as agencies could fit into their schedules. Overall, the results represent the first large-scale standardized sampling effort for bigheaded carp across four southeastern states and provide integral population information for natural resource managers. Future monitoring efforts should continue to track characteristics of bigheaded carp populations in the Tennessee and Cumberland rivers and determine effective control and management strategies for populations in large impoundments. </p><p>

<p> This thesis qualifies functional and ecological aspects of mucus trails deposited by <i>Elimia potosiensis</i> collected from the Meramec River. Freshwater snails are most often recognized for their significant role in river and stream ecosystem function as primary consumers and prey items. However, their form of locomotion is the most energetically expensive found in the animal kingdom. Found in large numbers and densities, <i> E. potosiensis</i> is capable of coating large swaths of substratum with carbohydrate- and protein-rich mucus. This has the potential to affect ecosystem function at the most basal trophic level both energetically, by contributing nutrients and energy to the surrounding water body, and functionally, as a sticky substance to which microheterotrophs become adhered. </p><p> In marine studies, researchers have found that bacteria can readily degrade gastropod mucus and that it can act as the basis for biofilm formation. There have also been studies that show unique employment of energy saving strategies by snails that use their trails to capture food items and to reduce production needs by following trails laid by conspecifics. Very little research has been conducted on freshwater gastropods. This study is the first to focus solely on the ecological and functional aspects of freshwater snail mucus. </p><p> For this study, collections of <i>E. potosiensis</i> were made from a single site along the Meramec River to qualify the effect deposited mucus has on the adherence of microalgae and its potential for formation of biofilms. Overall, mucus-coated surfaces significantly more particles in flow than non-coated surfaces. The water velocity at which a trail is laid was not found to have an affect on the thickness, adhesive ability or persistence of a trail. However, the water velocity in which a trail is incubated in stream does have effect on the adherence rate of a trail. In this study, it was found that this was most likely due to the fact that trails in high water velocity come into contact with more particles during a given period of time due, in part, to its higher carrying capacity.</p>