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Shade is defined as the coolness and darkness caused by shelter from solar radiation. In freshwater, shade is most commonly provided by riparian vegetation, which can affect water quality through its effects on temperature and light. The purpose of this research was to explore riparian shade influences on (1) fish distribution along reservoir littorals and (2) diel water quality patterns. Sampling was conducted in shaded and non-shaded paired sites in Columbus Lake, Mississippi, U.S.A. Differences in species distribution revealed that, in general, clupeids and most centrarchids were better represented in unshaded sites, while percids were better represented in shaded sites. Diel cycles of water quality variables were measured in situ over 24-h periods with auto-samplers and assessed using trigonometric polynomial regression to describe daily cycles. Analysis of covariance revealed all water quality variables differed between sites and most also varied between shaded and unshaded sites and exhibited daily cycles.

Doctor of Philosophy / Division of Biology / Keith B. Gido / This dissertation consists of three research-based chapters which focus on habitat association of prairie stream fishes and how these fish communities influence stream ecosystem properties. Chapter one introduces important concepts used throughout the chapters, and describes my study streams. In chapter two, I identify local habitat factors associated with the diversity and density of fishes in two protected prairie watersheds. Specifically, the relative importance of habitat factors associated with fish communities were evaluated along a stream-size gradient and across multiple seasons and years. I found that species richness was positively associated with pool area and discharge. Redundancy analyses showed common prairie fish species exhibit ontogenetic habitat associations, with adults in deep and juveniles in shallow pools. Chapter 3 addresses how fish species richness in small prairie streams affects whole-stream metabolism and biomass distribution of benthic organic matter, algal and macroinvertebrates. This study was conducted by stocking experimental stream mesocosms that included pool-riffle habitats with three different communities that represent a gradient of species richness of headwater prairie streams from one to three common prairie stream fish species. I illustrated how species influence ecosystems across multiple spatial scales and found that different communities altered the distribution of algal biomass from benthic surfaces to floating mats and from pools to riffles. The objective of the fourth chapter was to quantify how two size classes of herbivorous prairie stream fish species, central stoneroller Campostoma anamolum and southern redbelly dace Chrosomus erythrogaster differentially affect stream ecosystem properties. This study was also conducted in experimental stream mesocosms, where each unit consisted of one riffle and one pool. Using ANOVAs, I found large dace were associated with longer filaments (F = 7.5, P = 0.002, df = 4) and small fishes with less benthic organic matter (F = 4.2, P = 0.02, df = 4). There was no evidence for ontogenetic shifts in diet and likely differences in energetic requirements and behavior drove the differences among treatments. My research finds that small-bodied prairie stream fishes have predictable habitat preferences and effects on stream properties are dependent on species identity, richness and size structure.

Doctor of Philosophy / Department of Biology / Keith B. Gido / A fundamental goal of ecology is to understand environmental associations of species. These associations can provide a basis for predicting spatial distributions in contemporary habitats as well as how those distributions might change in response to anthropogenic environmental change. Developing species distribution models is limited by an incomplete understanding of functional traits, spatial scaling, and the mechanisms and generalities of correlations among abundance and environmental gradients. I address these four issues using observational and experimental approaches. First, I tested opposing mechanisms of community assembly by measuring the dispersion (i.e., diversity) of three types of functional strategies at three spatial scales and along environmental gradients. I found that communities are assembled via abiotic environmental filtering, but the strength of this filtering depends on the spatial scale of investigation, longitudinal network position, and type of functional strategy. Second, I quantified community-environment relationships across thirteen sub-basins, nested within the three major basins within Kansas to evaluate the consistency (i.e., generality) in predictive capability of environmental variables among sub-basins and across spatial extents. I found that longitudinal network position is consistently the strongest predictor of community composition among sub-basins, but in-stream and catchment predictors become stronger correlates of community composition with increasing spatial extent. Third, I used environmental niche models to quantify distributions of four pairs of congeneric cyprinids and found that species within each pair exhibited contrasting stream-size preferences. I then used field experiments to test for differences in individual-level performance between one pair of species (Pimephales notatus and P. vigilax) along a gradient of stream size. I found that adult spawn success and juvenile growth and condition increased with stream size for both species, indicating that these congeners respond similarly to abiotic gradients associated with the river continuum. I concluded that complementary distributions are a consequence of biotic interactions, differential environmental filtering evident in an unmeasured performance metric, or differential environmental filtering by an environmental factor operating at longer timescales. These studies demonstrate the context dependencies of characterizing habitat associations of stream fishes, but also reveal the general importance of stream size and associated environmental gradients in structuring stream fish communities.

Knowledge of biodiversity within an ecosystem is essential when trying to understand the function and importance of that ecosystem. A challenge when assessing biodiversity of reef habitats is cryptobenthic fishes, which encompass many groups that have close associations with the substrate. These fishes can be behaviorally cryptic, by seeking refuge within the reef matrix, or visually cryptic, using cryptic coloration to match the surrounding habitat. These factors make visual surveys inadequate for sampling these fishes. One such group of cryptobenthic fishes are the gobies, family Gobiidae, which currently represent over 1600 species, although new species are continually being discovered. Gobies are often small (less than 5 cm), and many species will be associated with a very specific microhabitat type. Due to the understudied nature of the Red Sea, little is known about habitat preferences of gobies within the region. In order to determine the differences in goby community structure within the central Red Sea, fishes were sampled at one reef using 1 m² enclosed rotenone stations from three distinct microhabitats: hard coral, rubble, and sand. Following collection, specimens were photographed and sequenced using COI, to aid in species identification. 232 individuals were collected representing 31 species of goby. Rubble microhabitats were found to host the majority of collected gobies (69%), followed by hard coral (20.6%), then sand (9.9%). Goby assemblages in the three microhabitats were significantly different from each other, and evidence of habitat-specialists was found. These results provide essential baseline information about the ecology of understudied cryptobenthic fishes that can be used in future large-scale studies in the Red Sea region.

Master of Science / Department of Biology / Keith B. Gido / Fishways are a common tool for mitigating the effects of habitat fragmentation on fish communities, but their utility in low-gradient, sand-bed rivers of the Great Plains is not well studied. The Lincoln Street Fishway on the Arkansas River became operational in 2015 and was built specifically to pass small-bodied threatened fishes. We used a combination of surveys up-and downstream of the barrier and tagging experiments to test the ability of fishes to move into and through the fishway. Differences in fish community structure up- and downstream of the dam were more pronounced prior to the construction and operation of the fishway. In particular, Emerald Shiner Notropis atherinoides was absent from collections upstream of the dam before fishway construction, but commonly collected upstream in 2015 and 2016 surveys. Surveys within the fishway structure revealed 29 species, or 74% of the total species captured during our study were using the fishway. To further quantify fishway passage, we used a VIE experiment to assess if fish marked downstream of the fishway moved into or upstream of the fishway. Although we did not recapture marked fish upstream of the fishway, some marked individuals moved into the fishway. Finally, we conducted a PIT tag experiment to evaluate short distance movements within the fishway for three species of small-bodied minnow and were able to document upstream movement across a gradient of flows through the fishway. Results from our study illustrate the potential for fishways to mitigate the effects of habitat fragmentation on small-bodied fishes in sand-bed rivers.

Aquatic biodiversity continues to decline as humans modify the landscape. A population-level approach is necessary to address the mechanisms of impairment in urban stream habitats. When estimating population-level parameters, incomplete detection of individuals must be accounted for to ensure unbiased estimates. In this thesis, I examined differences in the detection probabilities of stream fishes, and used estimates of size/age-specific detection probabilities to reduce bias in estimates of the reproductive success of various fish species in urban and forested stream habitats. In Chapter 1, I examined differences in detection probabilities of stream fishes among electrofishing passes and size/age groups in the middle New River basin, Virginia. I also examined differences in detection probabilities between two physiographic regions: the middle New River basin, and the upper Wabash River basin, Indiana; and evaluated differences between single- and multiple-season estimation methods. I found that for most species, detection probabilities do not differ among electrofishing passes, size/age classes, between the two regions, or between single- and multiple-season estimation methods. I used size/age-specific estimates of detection probabilities to remove bias from relative abundance estimates of steam fish populations in Chapter 2. In Chapter 2, I examined the reproductive success of six lithophilic and speleophilic fishes in urban and forested reaches of 2nd-4th Strahler-order streams in the middle New River basin. I found that binary classification is a poor method of quantifying reproductive success, that the age distributions of many lithophilic and speleophilic species are dominated by adult individuals in urban habitats, and that the population growth rates of speleophils is reduced in urban habitats. These results suggest that although detection probabilities may be equal among various sources of variation, managers should verify this assumption before assuming equal detectability. The results also suggest that reduced reproductive success of speleophilic and lithophilic species in urban stream habitats may be a mechanism of their impairment. / Master of Science

Master of Science / Department of Biology / Keith B. Gido / Recognizing habitat needs of fishes across space and time is increasingly important for managing altered stream networks, such as in the Colorado River basin. Recent work on warm-water fishes suggest they might benefit from access to tributaries and their confluences. Fish movements or distributions within tributaries relative to distance from mainstem confluences in two streams with different network types (linear versus dendritic) were investigated in the San Juan River basin, USA. Upstream distance from the San Juan River resulted in species declines (Chaco Wash, linear network) or turnover (McElmo Creek, dendritic network). McElmo Creek movement patterns were likely attributed to spring spawning migrations of flannelmouth sucker (Catostomus latipinnis), spawning aggregations of razorback sucker (Xyrauchen texanus), foraging or refuge seeking by Colorado pikeminnow (Ptychocheilus lucius), and monsoon-related movements for channel catfish (Ictalurus punctatus) and razorback sucker. Razorback sucker and Colorado pikeminnow dominated movements at Chaco Wash, suggesting this backwater-like tributary supplied thermal or current refuge, foraging habitat, or both. Within McElmo Creek, a second study explored the importance of confluences by characterizing habitat use and movements of fishes at the junction of McElmo and Yellow Jacket creeks. Native fish dominated the confluence community composition. The reach downstream of the confluence had consistently higher abundances, species richness, and more frequent detections of tagged fishes relative to upstream reaches. Movement behaviors inferred by detection frequency of tagged fish among reaches surrounding the confluence differed among species. Small flannelmouth sucker (< 300 mm) and roundtail chub (Gila robusta) were commonly detected in Yellow Jacket Creek whereas large flannelmouth sucker (> 300 mm), bluehead sucker (C. discobolus), and channel catfish used McElmo Creek reaches. Monsoons increased McElmo Creek discharge which triggered upstream movements of channel catfish and displaced large flannelmouth sucker and bluehead sucker. Monsoons increased movements between McElmo and Yellow Jacket creeks by roundtail chub, small flannelmouth sucker, and black bullhead (Ameiurus melas). Combined, these two field studies emphasized using links between patterns and processes of tributary fish communities. Conservation, rehabilitation, and maintenance of connectivity and habitat heterogeneity at confluence zones likely can be a localized management strategy with expansive ecosystem effects.