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Most northeastern river basins are stressed by the effects of development but the complexity of evaluating rivers often hinders the establishment of effective management regulations. Many methodologies have been proposed for assessing instream habitat, determining critical flow levels, and evaluating biological communities, but no one approach is universal. The overall objective of this thesis is to move towards standardizing components of river modeling. Rather than examine a full model, I investigated individual steps of MesoHABSIM, an instream habitat modeling approach. The two components studied involved applying the Reference Fish Community (RFC) method to identify a biological reference; and using depth and velocity data to standardize the description of hydraulic types. The RFC approach identifies the fish species and the expected proportions that should be present in a less impacted version of a river system. The Eightmile River watershed, was the focus of the study in which the RFC approach was employed to determine whether the fish community of this rural watershed, meets or exceeds a community developed using reference rivers. Similarity indices were used to identify differences between the existing (field-sampled) and expected communities. While the analysis of the Eightmile community indicates that it is in a better condition than the majority of rivers studied, it also shows some deviation from the reference, most likely due to elevated water temperatures and regional declines. The hydraulic type characterization study was developed to reduce the effort needed in depth and velocity measurement after this was identified as the most time consuming portion of the MesoHABSIM methodology. I used a series of pair-wise, independent-sample, Kolmogorov-Smirnov tests on a large bank of depth and velocity data to determine if patterns could be confirmed for each type of hydromorphological unit (HMU) across various streamflows. Few of the data sets were statistically similar enough to be combined and the mapping effort could not be simplified based on this investigation. Neither investigation provided the intended reference for the particular component of river modeling, further emphasizing the complexity in this area of study. However, the information gathered can be used as pioneering steps in future investigations.

Sedimentation and drawdown-induced habitat degradation limits reproduction of structure-associated fishes in flood control reservoirs. Littoral habitat enhancement can be accomplished by planting fast growing crops during winter, when lakebeds are exposed, to provide fish habitat during spring flooding. It remains unclear if species of crops differ in their submerged persistence or habitat quality to fish. I submerged six species of cool-season annual crops in mesocosms and monitored plant architecture over time. Adult plantings of two grasses persisted long enough to potentially be used by juvenile fishes in reservoirs. To assess the habitat quality provided by crops, I evaluated selection by juvenile Bluegills and adult Largemouth Bass in outdoor mesocosms. Bluegills selected Balansa Clover the most and Largemouth Bass selected annual Ryegrass. Results suggest some clovers may provide nursery habitat but degrade rapidly once submerged and dense annual grasses persist well and provide favorable habitat for prey and predator fish.

<p>Coastal wetlands are hydrologically connected to their watershed and the lake. Water levels in Georgian Bay have been at a sustained low for thirteen years and thus connectivity of wetlands to the lake is being threatened as water levels decline. Decreased connectivity has likely caused changes in ecological and chemical characteristics. Future climate change models predict further water declines and potentially increasing the number of wetlands that will be hydrologically disconnected. The over-arching goal of this thesis is to investigate the role of connectivity between the lake and coastal marshes in eastern Georgian Bay on the amount of potential fish habitat, water chemistry and larval amphibian habitat.</p> <p>Bathymetric information is needed in order to estimate fish habitat and two approaches were utilized in order to collect these data. A site-specific method completed in 2009 used an intensive field survey in seven wetlands to create a digital elevation model and calculated the amount of fish habitat at 10 cm increments. A second, regional method, selected 103 sites by using a stratified random sample in 18 quaternary watersheds. In both methods, changes in water levels between 173 and 176 m asl resulted in the most drastic loss of habitat. Approximately 24% of the current fish habitat has already been lost due to low water levels.</p> <p>Water chemistry in coastal marshes is influenced by hydrologic connection. In the summers of 2010 and 2011, 35 coastal marshes were sampled, 17 of which had been impounded and disconnected by a beaver dam. Beaver-impounded marshes resulted in significantly lower pH, conductivity, dissolved oxygen and sulphate concentrations, but had significantly higher soluble reactive phosphors concentrations. These conditions are indicative of the lack of connection and reduced mixing with lake water. This altered habitat was shown to support breeding area for 7 species of amphibians, the most common being green frogs and the least common being American Toads and chorus frogs.</p> / Master of Science (MSc)

The goal of this research was to formulate new tools for instream-flow analyses, with emphasis on protecting fish assemblages in speciose, warmer-water streams. This included habitat and fish data sets for the upper Roanoke River (URR) in southwestern Virginia, collected during the warmer, low- f low seasons of 1989-1991. Physical data were collected in small, rectangular quadrats or crosssectional transacts, whereas fish were collected by seining and electroshocking in the quadrats. Statistical analyses included uni-, bi-, and multivariate analyses. The habitat analyses showed that mesohabitat types could be effectively defined with hydraulic, channel-roughness, and geomorphologic variables, and different habitat types showed characteristically different hydraulic dynamics across flows. The analyses also showed that physical habitat could be effectively described by 4 axes (sets of similar variables) at microhabitat scales, although greater covariation occurred at intermediate spatial scales (meso- and macrohabitat level). Habitat assessment for instream-flow analyses can thus be effectively simplified by undertaking visual assessment of several mesohabitat types and/or by measuring only a few physical variables for microhabitat analyses. The differences in hydraulic dynamics among mesohabitat types can simplify determination of changes in the availability of fish habitat across flows. The fish analyses showed that habitat-use guilds of fish species could be effectively defined with aggregated data, i.e., across mesohabitat types or by calculation of fishes' habitat-use means for physical variables. In contrast, unaggregated data (each quadrat considered separately) gave cruder habitat-use segregation of fish species, particularly because fish species were independent of each other at smaller spatial resolutions and larger spatial extents. The 7 guilds included 4 rheophilic (riffle-oriented) and 3 limnophilic groups (pooloriented). Habitat-suitability models developed for these guilds showed that fish selected habitat variables independently, such that simple models can be developed to predict fish abundance in response to differences in habitat availability. In sum, the analyses provided habitat-flow and fish-habitat data that can be interfaced (in future analyses) to predict changes in fish abundance and biodiversity to be expected from permanent changes in flow levels and thus habitat availability. / Ph. D.

The SNTEMP (U.S. Fish and Wildlife Service), QUAL2E (U.S. Environmental Protection Agency), and RQUAL (Tennessee Valley Authority) stream temperature prediction models were evaluated. All models had high predictive ability with the majority of predictions, >80% for Back Creek (Roanoke County, VA) and >90% for the Smith River tailwater (SRT) (Patrick County, VA), within 3°C of the measured water temperature. Sensitivity of model input parameters was found to differ between model, stream system, and season. The most sensitive of assessed parameters, dependent on model and stream, were lateral inflow, starting-water, air, and wet-bulb temperature. All three models predicted well, therefore, selecting a model to assess alternative water management scenarios was based on model capabilities. The RQUAL model, used to predict SRT temperatures under alternative hydropower release regimes, illustrated potential thermal habitat improvement for brown trout (Salmo trutta) compared to existing conditions. A 7-day/week morning 1 hr release was determined to best concurrently increase occurrence of brown trout optimal growth temperatures (+10.2% mean), decrease 21°C (state standard) exceedances (99% prevention), and decrease hourly changes in temperature (-1.6°C mean) compared to existing thermal conditions. The SNTEMP model was used to assess thermal habitat under flow, shade, and channel width changes occurring from future urbanization within the Back Creek watershed. Predictions reveal that additional urban development could limit thermal habitat for present fish species by elevating summer mean daily temperature up to 1°C and cause 31°C (state standard) exceedances compared to existing conditions. Temperature impacts were lessened by single rather than cumulative changes suggesting mitigation measures may maintain suitable thermal habitat. / Master of Science

Using a towed underwater video camera system, benthic habitats were classified along transects in a popular offshore fishing area on the West Florida Shelf (WFS) known as “The Elbow.” Additionally, high resolution multibeam bathymetry and co-registered backscatter data were collected for the entire study area. Using these data, full coverage geologic and biotic habitat maps were developed using both unsupervised and supervised statistical classification methodologies. The unsupervised methodology used was k-means clustering, and the supervised methodology used a random forest algorithm. The two methods produced broadly similar results; however, the supervised methodology outperformed the unsupervised methodology. The results of the supervised classification demonstrated “substantial agreement” (κ>0.6) between observations and predictions for both geologic and biotic habitat, while the results of the unsupervised classification demonstrated “moderate agreement” (κ>0.4) between observations and predictions for both geologic and biotic habitat. Comparisons were made with the previously existing map for this area created by Florida Fish and Wildlife Conservation Commission’s Fish and Wildlife Research Institute (FWC-FWRI). Some features are distinguishable in both maps, but the FWC-FWRI map shows a greater extent of low relief hard bottom features than was predicted in our habitat maps. The areas predicted as low relief hard-bottom by FWC-FWRI often coincide with areas of higher uncertainty in the supervised map of geologic habitat from this study, but even when compared with ground-truth points from the towed video rather than predictions, the low relief hard bottom in FWC-FWRI’s map still corresponds to what was identified as sand in the video 73% of the time. The higher uncertainty might be a result of the presence of mixed habitats, differing morphology of hard-bottom, or the presence of sand intermixed with gravel or debris. More ground-truth samples should be taken in these areas to increase the confidence of these classifications and resolve discrepancies between the two maps. Data from the towed video system were also used to assess differences in fish communities among habitat types and to calculate habitat-specific densities for each taxa. Fish communities were found to significantly differ between soft and hard bottom habitats as well as among the hard-bottom habitats with different vertical relief (flat hard-bottom vs more steeply sloping areas). Additionally, significant differences were found between the fish communities in habitats with attached fauna such as sponges and gorgonians, and areas without attached fauna; however, attached fauna require rock to attach to and the rock habitats rarely lacked attached fauna, so this difference may just reflect the difference between fish communities in sand and rock habitats without the consideration of vertical relief. Moreover, the species driving the differences in the fish communities were identified. Fish were more likely to be present and assemblages were more species rich in more complex habitats (rockier, higher relief, presence of attached fauna). Habitat specific densities were calculated for each species, and general trends are discussed. Lastly the habitat-specific densities were extrapolated to the total area of habitat type (sand vs rock) as predicted by the supervised geologic habitat map. There is predicted to be approximately 111,000 fish (95% CI [67015, 169405]) within the study area based on this method, with ~47,000 (~43%) predicted to be within the sand habitat and ~64,000 (~57%) in the rock habitat. This demonstrates the potential of offshore rocky reefs as “critical habitats” for demersal fish in the offshore environment as rock accounts for just 4% of the study area but is expected to contain over half of the total abundance. The value of sand habitats is also shown, as due to their large area they are able to contribute substantially to the total number of fish despite sustaining comparatively low densities.

Responses of juvenile steelhead trout to changes in stream habitat resulting from an instream habitat rehabilitation project in Meadow Creek, Oregon were measured from 1991 through 1992 and compared to pre-treatment data from 1987 through 1990. Sixty nine pool-forming, and 59 channel-stabilizing log structures were constructed by the U.S. Forest Service in a 3.7 km reach in 1990. A 20-year flood caused extensive modifications to the instream structures in May 1991. Pool habitat and large wood volume increased in the treatment and the two reference reaches but pool development was greater in the treatment reach compared to the two reference reaches. Summer rearing densities of juvenile steelhead were similar for the treatment and the two reference reaches at the reach scale. Summer rearing densities were lower in the post-treatment period compared to the pre-treatment period for the treatment and two reference reaches. Mean density of juvenile steelhead was higher in complex pools compared to non-complex pools throughout the study area. Mean density of juvenile steelhead was higher in pools associated with large wood from washed-out structures compared to pools associated with intact structures in the treatment reach. Changes in smolt production from the treatment reach following the rehabilitation project could not be determined due to trapping difficulties. Only three percent of the smolts emigrating from the basin overwintered in the treatment reach in 1992. Four life history patterns of juvenile steelhead were identified. Only one of the four life history patterns rears in the Meadow Creek basin until smolting. From these findings I conclude that the instream habitat rehabilitation project did not increase the abundance of juvenile steelhead or smolt production during the first two years after treatment. An extended drought and a 20-year flood may have been the dominant factors controlling abundance of juvenile steelhead over the study period. The Meadow Creek rehabilitation project may have limited success at increasing smolt production because it influences only one of four life history patterns of juvenile steelhead during the entire freshwater rearing phase. / Graduation date: 1997

Thesis (Ph.D.)--Mississippi State University. Department of Wildlife and Fisheries. / Title from title screen. Includes bibliographical references.