Understanding the composition of lotic communities and the landscape processes and habitat characteristics that shape them is one of the main challenges confronting stream ecologists. In order to better understand the linkages among landscape processes, stream habitat, and biological communities and to understand how accurately our measurements represent important factors influencing biological communities, it is important to test explicit hypotheses regarding these linkages. Increasing our understanding of aquatic communities in a hierarchical context and recognizing how well our measurements represent factors structuring aquatic communities will help managers better evaluate the influence of land management practices on aquatic ecosystems, direct conservation strategies, and lead to better assessments of ecological condition. In Chapter 2, we used spatial data, field-based habitat measurements, and macroinvertebrate community data to 1) examine the influence of landscape processes on two factors of stream habitat; maximum stream temperatures and fine sediment, and to 2) examine how well these landscape and habitat characteristics represent factors influencing gradients in macroinvertebrate community structure. The results of this study showed that spatially derived measurements may be effectively used to test hypotheses regarding landscape influences on stream habitat and that spatial data, used in conjunction with field measurements can provide important information regarding factors influencing gradients in biological communities. In addition, spatially derived measurements may provide the same or additional information regarding influences on community structure as field-based measurements, which suggests that further research should be done to assess how well our field measurements represent factors that are important in shaping stream communities. The objective of Chapter 3 was to compare how well single field measurements and a combination of indicator variables hypothesized to be components of a single ecological processes or concept, known as a latent variable, represent thermal stress and fine sediment influences on macroinvertebrate communities. Results from this study showed that both single and latent variables explained relatively the same amount of variation in macroinvertebrate community structure. This suggests that while latent variables may have a potential to better refine how we represent ecological factors, a better basis for defining a priori hypotheses is needed before these variables can provide any additional information compared to single habitat measurements.

Estimates of production and related parameters (growth rate, density, standing crop) were made for populations of mountain whitefish in altered and "unaltered" areas of the Glacksmith Fork and Logan River, UtJh from spring 1975 through summer 1976. Capture records of marked whitefish were also analyzed to describe fish movement and check on assumptions implicit in the population estimator. Mean weights and instantaneous growth rates of whitefish were similar at all sites for comparable size/age groups. Among sites, differences in production per sampling interval and annual production were due mainly to differences in standing crop and/or age structure. Estimates of mountain whitefish density varied by site and season and ranged from 0 to 3,467 fish/ha, with the highest densities occurring during the fall and winter (spawning season) and the lowest during the summer when streamflows were low. Estimates of standing crops of whitefish followed a pattern similar to density. In the sites where fish remained during the summer most production occurred during the spring and summer. A bulldozed reach of the Logan River (including an "unstable" section) had the highest annual production of mountain whitefish (51.85 kg/ha/yr)--almost double the annual production for the same reach when the unstable section was not included (31.85 kg/ha/yr). The highest annual production of whitefish in sites in the Blacksmith Fork River (51.23 kg/ha/yr) occurred in a reach that had been recently dredged but still contained a riffle and pool structure. Annual production of whitefish was low in a recently bulldozed reach (5.47 kg/ha/yr) and an old bulldozed reach (10.08 kg/ha/yr) of the Blacksmith Fork River where suitable habitat (pools and glides) was lacking, especially during the summer months. Mountain whitefish remained or returned to reaches after channel alterations as long as water depth remained sufficient. This study illustrated the necessity of frequent sampling when attempting to evaluate the effects of perturbations on fish populations or in production studies in general.

Estimates of the brown trout (Salmo trutta) population were made in two areas of the Blacksmith Fork River, Cache County, Utah, from June 1972 to June 1973. Additional data were obtained on movement, growth, mortality, biomass, production, and yield. Population density was highly variable in the area where habitat alterations had occurred, but was relatively uniform where the habitat was undisturbed. The brown trout exhibited little movement except during spawning season. Instantaneous growth and mortality rates are provided for each age group. Mean annual biomass in the two areas was 12.0 and 10.2 grams per square meter and production was estimated at 9.2 and 7.7 grams per square meter per y ear in the two study areas. Gametes comprised approximately 5 percent of the annual production and angler harvest removed 39 percent of production.

Microcystin-LR is a hepatotoxin produced by cyanobacteria. Aeromonas hydrophila and Edwardsiella piscicida infections are leading causes of losses in market-sized channel catfish (Ictalurus punctatus). These older fish should have natural immunity in place and a predisposing factor is likely a prerequisite for these disease outbreaks. While microcystin-LR rarely causes mortality in warm-water aquaculture, we believe it may be a predisposing factor that leads to bacterial disease outbreaks during the summer months due to its ability to damage the liver. Our study investigated microcystin-LR’s effects on channel catfish susceptibility to these pathogens. We found that a sublethal dose of microcystin-LR induced substantial damage to multiple immune organs. In our challenges with both the toxin and bacteria, we saw a significant increase in mortality of fish. Our findings suggest that microcystin-LR increases channel catfish susceptibility to Aeromonas hydrophila and Edwardsiella piscicida infections.

Conserving and restoring anadromous fish populations is an important research and management priority. For conservation to be effective, researchers must understand the behavior of the fish they seek to restore. Telemetry has allowed researchers to understand the upstream migrations of these fish in freshwater, how migration patterns vary, and if there is a relationship between behavior and environmental variables. In the northeastern United States, alewife (Alosa pseudoharengus), one of two species collectively referred to as river herring, has historically been an important component of coastal rivers. However, populations of these fish have experienced recent declines, and a commonly used method to restore river herring is stocking. In this thesis, I summarize research that seeks to understand anadromous alewife behavior with the goal of providing insights that will help manage and conserve this species and the coastal systems in which they live. My thesis has a primary research chapter (Chapter 1), a second ancillary research chapter (Chapter 2), and four appendices that summarize related information as part of the funding proposal. First, to examine if fish origin (native or stocked) and fish release location (upstream or downstream) affected the pre-spawning movements of fecund alewives, I undertook a reciprocal experiment. In Chapter 1, for fish of both origins and release locations, I examined how long fish were in the river, where they spent their time, and how much and how fast they moved. For this, I gastrically tagged alewives with Lotek Nanotags NTC-6-1 radio tags and monitored movements in the lower 30 km of the Ipswich River (northeastern Massachusetts) using an array of 9 Lotek SRX_400 receivers. Based on these movement trajectories I concluded that in 2007, origin affected the total time fish spend in the river and release location affected where they spend their time. Downstream movements of upstream migrating fish have typically been viewed as a behavioral assay of adverse tag effects. For this reason, alosine telemetry studies rarely release tagged fish upstream of the capture site. However, fisheries managers often release fish upstream near spawning grounds during stocking. In Chapter 2, I re-evaluated whether downstream movements of upstream stocked fish were consistent with an adverse tag effect. By combining physiological experiments with select movement trajectories, I showed that pre-spawning migrations of alewife included an array of up and downstream directed movements with various interpretations. In my research, these downstream movements were unlikely to be related to tagging stress (Chapter 2), as the cortisol, glucose, and chlorides of tagged fish were not different from untagged fish (Appendix A, Physiology). Furthermore, I suggested metrics that should be recorded in telemetry studies to standardize how downstream fish movements are measured. In 2006, native fish were released at a downstream site (river km 6) and stocked fish were released upstream (rkm 25). I compared the behaviors of these same treatments across years. I showed that the behaviors of fish released in different years may differ based on temperature and discharge (Appendix B, Across Year Comparison). To determine the amount and location of potential spawning habitat, I undertook a habitat study that utilized a geographic information system (GIS) to maps the size and distribution of habitat types. I located multiple mainstem pools in the Ipswich River that may serve as suitable spawning grounds for alewife. Tagged fish were primarily located in these habitats (Appendix C, Habitat). To determine if juveniles were produced, I sampled various sites in the river for the presence of juveniles, using active and passive sampling techniques. Juveniles were not captured during these surveys (Appendix D, Juvenile Sampling). Before this research, little was known about the pre-spawning migrations of river herring. While river herring are assumed to be a generalist species, I found their behaviors to be complex. I have identified a number of gaps in the current knowledge of how these fish behave in the field. Restoration efforts must take into account the behavior of the fish, as well as the capacity of a system to accommodate those needs. Within the context of understanding fish behavior, protecting habitat, and providing regulatory restrictions on the fishery, stocking may contribute to broader management and restoration goals.

Exploratory research into a fresh concept, building integrated aquaculture, has found new information on the topic. Motives indicating building integrated aquaculture is important for sustainable development were identified. A review of the literature found relatively little in the way of experiments, aquaculture operations, and case studies which documented or demonstrated a deep understanding of the interactions between building and aquaculture systems. A simple experiment was conducted observing thermal energy and moisture interactions in simulated aquaculture facilities, some with tank covers and insulation. Two different retrofit programs were developed in a case study of building integrated aquaculture for an existing structure on the campus of the University of Massachusetts.

Despite the threat of climate change, the physiological mechanisms by which temperature drives the distribution of species are unclear. Here we used chronic temperature exposures to determine that the upper limit for positive growth in the eastern brook trout (Salvelinus fontinalis) is 23.4 °C. Additionally, brook trout exposed to daily temperature oscillations of 8 °C, around a mean of 21 °C, exhibited growth rates that were 43 and 35% lower by length and weight respectively, than in constant 21 °C controls. Limitations in growth were associated with increases in indicators of the physiological stress response. Individuals exposed to 22 or 24 °C for 24 days exhibited plasma cortisol levels that were 12 and 18 fold greater than at 16 °C. Similarly, gill heat shock protein (Hsp)-70 levels were 10.7 and 56 fold higher at 22 and 24 °C than at 16 °C. Brook trout exposed to daily temperature oscillation of 4 or 8 °C had gill Hsp-70 levels that were 40 and 700 fold greater than controls. Acute (6 h) temperature exposures were used to demonstrate a threshold for induction of the Hsp-70 and plasma glucose responses of 20.7 °C and 21.2 °C respectively. Finally, we conducted field surveys that demonstrated increased plasma cortisol, plasma glucose, and gill Hsp-70 at temperatures above 21 °C. Induction of the cellular and endocrine stress responses is associated with decreased growth in brook trout. Thermal limitations on growth may provide a mechanism by which temperature drives the distributions of this cold-water species.

The hills of Yazoo Basin have a long history of land use modification and subsequent erosion and flood control issues. In response, federal actions were taken to address these issues beginning after the Mississippi River flood of 1927. Four major flood control reservoirs were built in 1932-1957, and instream low-drop grade control structures (GCS) were installed beginning in the 1980s. The objective of my dissertation was to ascertain the long-term effects of these efforts on stream fish assemblages and channel morphology. To assess whether the reservoirs affected upstream fish assemblages as barriers to recolonization by fluvial fishes or as source population for invasion by lentic generalist fishes (Chapter 1), I used stream data collected 43-61 years after the rivers were impounded to test for differences in fish assemblages between sites upstream and downstream of the reservoirs. Analysis of catch per effort and diversity metrics displayed little influence of the reservoirs, but trait-based analysis revealed marginal increases in planktivores, herbivores, detritivores, and generalists in upstream assemblages. After determining that potential effects of reservoirs would not confound further analysis, I assessed the effects of GCS on channel morphology (Chapter 2) and fish assemblages (Chapter 3) 30 years post-installation. To assess GCS effects on channel morphology, stream cross-sections were used to calculate Bank Height Ratio, Width/Depth Ratio, and Entrenchment Ratio, while point estimates made along the transects were used to calculate the average sediment size distribution. Analyses revealed that the GCS were successful in checking channel incision moving headward in the streams: sites upstream of the GCS were less incised and had greater accumulations of fine substrates compared to downstream sites and sites on streams lacking erosion control structures. The GCS could potentially affect fish assemblages through habitat modification or by selectively filtering the assemblages as a barrier to upstream migration. Analysis of beta diversity revealed that diversity was driven by species replacement rather than nestedness, which indicates GCS were not acting as filters on the assemblages. Analysis of catch per effort data confirmed differences in assemblage structure that echoed the instream habitat differences revealed in Chapter 2.

Over the last century anadromous alewife (Alosa psuedoharengus) and blueback herring (Alosa aestivalis), collectively called river herring, suffered drastic declines throughout their range from Newfoundland (Canada) to North Carolina (USA). A 2011 petition to include river herring in the Endangered Species Act (ESA) was rejected, partly due to inadequate information towards identifying coast-wide population status. Additionally, knowledge gaps were identified with basic ecology of the river herring life cycle in freshwater, including species reproductive strategies. In Chapter 2, I investigated how body size, spawning arrival time, and sex influence river herring reproductive success. I collaborated with the Massachusetts Division of Marine Fisheries to introduce adult river herring (421, 266, and 410 individuals in 2013, 2014, and 2015, respectively) into Pentucket Pond (Massachusetts, USA), which historically had river herring but is currently inaccessible to upstream migrants. Using fin clips from stocked adult fish and juveniles collected in the lake each summer, I genotyped individuals and constructed pedigrees with 15 microsatellites. River herring had small (mean =1.1) families and spawned multiple times with multiple mates from May to June. Females were more successful than males. Earlier arrival and larger body size were independent indicators of reproductive success. These results provide critical river herring life history information for the freshwater component of population models that will inform management of this at-risk species. Presently, most river herring populations are monitored using data from citizen counts of spawning adults entering freshwater. Involving citizen watershed groups in data collection and may provide ancillary benefits beyond collection of population-level count data. In Chapter 3, I used pre-and post-surveys to assess how involvement in one citizen monitoring program influenced participants’ environmental knowledge, attitudes, and behaviors. Participants began the program with high scores for broader scientific and pro-environmental attitudes and pro-environmental behaviors. After the program, participants reported increased connection to nature, citizen science involvement, river herring knowledge, and engagement in outdoor recreation. For participants, engagement with nature was the most important program benefit. These results provide an additional case study to the citizen science literature and demonstrate that citizen science programs can help participants connect with the environment.

Biodiversity monitoring and predictions of species occurrence are essential to develop outcome-oriented conservation management plans for endangered species and assess their success over time. To assess distribution and patterns of habitat use of large mammal assemblages in Thailand, with a focus on the endangered dhole (Cuon alpinus), I first implemented a long-term camera-trapping project carried out with park rangers from October 2003 through October 2007 in Khao Yai National Park. This project was extremely successful and may serve as a regional model for wildlife conservation. I found significantly lower relative abundance indices for carnivore species, and collectively for all mammals compared to data obtained in 1999-2000, suggesting population declines resulting from increased human activity. I integrated this data into maximum entropy modeling (Maxent) to further evaluate whether ranger stations reduced poaching activity and increased wildlife diversity and abundances. I then conducted a focused camera trap survey from January 2008 through February 2010 in Khao Ang Rue Nai Wildlife Sanctuary to gather critical baseline information on dholes, one of the predator species that seemed to have declined over time and that is exposed to continued pressure from humans. Additionally, I led a collaborative effort with other colleagues in the field to collate and integrate camera trap data from 15 protected areas to build a country-wide habitat suitability map for dholes, other predators, and their major prey species. The predicted presence probability for sambar (Rusa unicolor) and leopards (Panthera pardus) were the most important variables in predicting dhole presence countrywide. Based on my experience from these different field ecological surveys and endeavors, it became clear that local people's beliefs may have a strong influence on dhole management and conservation. Thus, I conducted villager interview surveys to identify local attitudes towards dholes, document the status of dholes in wildlife sanctuaries adjacent to Cambodia, and determine the best approach to improve local support for dhole conservation before proceeding with further field studies of the species in Thailand. A photograph of a dhole was correctly identified by only 20% of the respondents. My studies provide evidence that some protected areas in Thailand continue to support a diversity of carnivore speices of conservation concern, including clouded leopards (Neofelis nebulosa), dholes, and small felids. However, dholes' impact on prey populations may be increasing as tiger (Panthera tigris) and leopards are extripated from protected areas. The next step in dhole conservation is to estimate the size and stability of their fragmented populations and also focus on maintaining adequate prey bases that would support both large felids and dholes