The ability of an organism to disperse to suitable habitats, especially in modified and fragmented systems, determines individual fitness and overall population viability. The bluehead sucker (Catostomus discobolus), flannelmouth sucker (Catostomus latipinnis), and roundtail chub (Gila robusta) are three species native to the upper Colorado River Basin that now occupy only 50% of their historic range. Despite these distributional declines, populations of all three species are present in the San Rafael River, a highly regulated tributary of the Green River, Utah, providing an opportunity for research. Our goal was to determine the timing and extent of movement, habitat preferences, and limiting factors, ultimately to guide effective management and recovery of these three species. In 2007-2008, we sampled fish from 25 systematically selected, 300-m reaches in the lower 64 km of the San Rafael River, spaced to capture the range of species, life-stages, and habitat conditions present. We implanted all target species with a passive integrated transponder (PIT) tag, installed a passive PIT tag antennae, and measured key habitat parameters throughout each reach and at the site of native fish capture. We used random forest modeling to identify and rank the most important abiotic and biotic predictor variables, and reveal potential limiting factors in the San Rafael River. While flannelmouth sucker were relatively evenly distributed within our study area, highest densities of roundtail chub and bluehead sucker occurred in isolated, upstream reaches characterized by complex habitat. In addition, our movement and length-frequency data indicate downstream drift of age-0 roundtail chub, and active upstream movement of adult flannelmouth sucker, both from source populations, providing the lower San Rafael River with colonists. Our random forest analysis highlights the importance of pools, riffles, and distance-to-source populations, suggesting that bluehead sucker and roundtail chub are habitat limited in the lower San Rafael River. These results suggest management efforts should focus on diversifying habitat, maintaining in-stream flow, and removing barriers to movement.

We exposed a native endangered species, bonytail chub (Gila elegans), to graded concentrations of secondarily-treated effluent. At the end of each treatment period, we collected water from all raceways and samples were analyzed for the presence of 83 organic wastewater compounds. We extracted blood plasma from control and treatment fish in each raceway and samples were analyzed for hormones, 17β-estradiol and 11-ketotestosterone, and the egg yolk protein, vitellogenin.17β-estradiol concentrations were consistently lower in treatment females than those detected in control females. The 17β-estradiol and vitellogenin concentrations were always higher in treatment males than those found in control males. Concentrations of 11-ketotestosterone were consistently lower in treatment males than those detected in control males.Endocrine disrupting effects occurred in male and female fish exposed to low concentrations of effluent. Changes in hormone levels suggested a feminizing effect in treatment male fish and an androgenizing effect in treatment female fish.

Thesis (M.S.)--University of Wyoming, 2007. / Title from PDF title page (viewed on Feb. 17, 2009). Includes bibliographical references (p. 64-79).

Without an adequate understanding of complex interactions between native and non-native species, management of invasive species can result in unforeseen detrimental impacts. I used both field and laboratory experiments to study reciprocal species interactions between the endangered Mohave tui chub (Siphateles bicolor mohavensis) and invasive western mosquitofish (Gambusia affinis). I also examined the impacts of both fish species on the aquatic invertebrate communities in desert springs. I demonstrate a case of intraguild predation (IGP) as a mechanism facilitating co-persistence of the endangered Mohave tui chub with invasive mosquitofish using field mesocosm experiments. In this case of IGP, adult tui chub prey on adult and juvenile mosquitofish, while adult mosquitofish prey on tui chub eggs and/or larvae. I conducted laboratory predation trials to assess if IGP was size-structured due to predator gape-limitation. I explored sex specific differences in gape-size limitation in mosquitofish, because mosquitofish are sexually dimorphic. Larval tui chubs had lower survival in the presence of female mosquitofish than in the presence of males. Reciprocally, male mosquitofish had lower survival than the females in the presence of Mohave tui chub. These results combined with vulnerability modeling supported that IGP in this system is size structured based on gape-size limitation. These results collectively suggest size-structured IGP may facilitate the co-persistence of these two fish species. My findings also suggest that mosquitofish may not be a limiting factor for the persistence of the endangered Mohave tui chub. Further, habitats currently harboring mosquitofish were considered as future refuge habitats for Mohave tui chub, a management option previously un-available. In addition to such reciprocal interactions between fish species, recently established fish populations may impact unique invertebrate communities. Mesocosm experiments with sympatric and allopatric populations of tui chub and mosquitofish showed negative impacts of both fish species on changes of invertebrate community structure. Specifically, fish caused population declines and, in some cases, extirpations of various invertebrate taxa. These results suggest important conservation implications of invasive fish as well as protected fish transplants into fishless desert springs. Overall my research emphasizes the complexity of ecological interactions between native and non-native fish species in desert aquatic systems.

The reproductive biology of the least chub Iotichthys phlegethontis (Cope) was studied from June 1976 to March 1978. Fish from both field and laboratory populations of the Leland Harris Spring Complex, Juab Co., Utah were utilized in the study. Reproduction in 1977 occurred from April to July in the field population and from April through August in the laboratory population. Reproduction was determined from gross examination and weight measurements of testes and ovaries, breeding coloration in males and diameter measurements of ova. Males and females matured at about the same size, 28 to 30 mm TL. The number of mature ova produced during spawning ranged from 283 to 2752 for females 31 to 46 mm TL. Mature ova ranged in size from 0.8 to 1.28 mm. Least chub are partial and intermittent spawners. This conclusion is supported by ova diameter measurements and calculations of the duration and peak period of spawning. Least chub are polyandrous broadcast spawners over vegetation. The eggs are demersal and adhesive. The egg incubation period was 2.1 days at 22.2 C. The eleutheroembryo are approximately 4 mm in length. They are not photophobic and appear to have cement glands. Specific characteristics of reproduction are discussed in relation to ecological conditions of the habitat.

The presence of fine muddy sediment (grain size < 0.1 mm) in streams has many impacts on the fluvial system and those relying on it, both humans and aquatic biota. Previously, fine sediment was considered a washload and has been ignored in transport models. More recently, it has been treated as being transported once the surface gravel layer that stores it is able to be mobilized. We propose that the surface layer need not be mobilized in order for muddy sediment to travel through the fluvial system in a series of erosive and depositional events. Our first study uses a new in situ device to show how mud entrainment from immobile gravel beds behaves cohesionlessly and can be modeled using the framework of classic sand-based models modified to account for hiding effects present in the stream bed. It also provides a method to predict how deep into the surface layer of gravel entrainment of fine sediment will occur given flow and stream bed characteristics. The second study investigates the primary pathway that fine sediment is traveling to get captured within bluehead chub fish nests. It was determined that more deposition of mud occurred in the upstream half of the nest concluding that the primary pathway was hyporheic pumping through the nest. Capture efficiencies of the nests were also found to increase as the length of nests increased. Both of these studies provide supporting evidence in the need to transition modeling fine sediment transport as a series of deposition and resuspension. / Master of Science / Fine muddy sediment (grain size < 0.1 mm) is present in natural streams and has many impacts on the stream system and those relying on it, including humans, plants, animals, and other organisms in the ecosystem. Previously, fine sediment was treated as being too small to consider in models that aid in understanding how a stream transports sediment. This is because small sediment stays suspended in the water column more easily than larger sediment. Therefore, it was just assumed to pass through the system and never deposit into the stream bed. However, in nature we observe large quantities of fine sediment being stored within the stream bed. More recently, it has been assumed that the sediment that does deposit will be transported once the surface gravel layer that stores it is able to be mobilized. That is, the surface gravel layer shields the fine sediment trapped between it and that the mud will stay put until that gravel is moved. We propose that the surface layer need not be mobilized for muddy sediment to travel through the fluvial system in a series of erosive and depositional events. Our first study uses a new device that forces erosion of mud to show how mud entrainment, or the process of how a fluid picks something up and carries it, from immobile gravel beds can be modeled using the framework of classic sand-based entrainment models modified to account for hiding effects, or protection against entrainment of a smaller sediment by a larger sediment shielding it, present in the stream bed. It also provides a method to predict how deep into the surface layer of gravel that fine sediment will be eroded given flow and stream bed characteristics. This is beneficial in estimating the amount of sediment that will be eroded during a given storm event. The second study investigates the primary pathway that fine sediment is traveling to get captured within bluehead chub gravel fish nests used for spawning their eggs and reproducing. It was determined that more deposition of mud occurred in the upstream half of the nest. This leads us to believe that the primary pathway of sediment traveling through the nest was hyporheic pumping through the nest, or the process of water flowing down through the surface layers of sediment in the stream bed. Capture efficiencies, or the ratio of how much of the sediment that traveled through the nest was captured, of the nests were also found to increase as the length of nests in the downstream direction increased. Both of these studies provide supporting evidence in the need to transition modeling fine sediment transport as a series of deposition and resuspension.

The bluehead chub (Nocomis leptocephalus) is a keystone species, an ecosystem engi- neer that constructs mounded gravel nests for spawning. Chubs provide benefits for other spawning fishes, predators, and benthic organisms through their nest construction. This study seeks to apply sediment transport models to find incipient motion criteria and erosion susceptibility of chubs nests. Field water flow velocities were measured with an acoustic Doppler velocimeter (ADV) in Tom's Creek, Blacksburg, Virginia, USA. ADVs are often used to collect in-situ turbulent velocity data. In almost all applications of ADVs, erroneous spikes are recorded during collection, which can significantly distort turbulence statistics de- rived from velocity fluctuations. In this study, a bivariate kernel density estimation despiking algorithm is compared to a novel univariate simplification developed as part of this work. Despiking methods are evaluated using field ADV and direct numerical simulation (DNS) data of a turbulent boundary layer. Visual assessment of despiked velocity time series and power spectra and corresponding changes in statistical moments, as well as response to arti- ficial spiking of DNS data, yield valid performance of the univariate method. After despiking chub nest data, multiple methods of finding bed shear stress from velocity vertical profiles are evaluated. Bed shear stress is found over the profile of 26 field nests. The ambient to peak flow stress amplification due to a nest's bed protrusion is found to be a proportion of τ = 1.66τ to determine a critical ambient Shields parameter of approximately τ∗ = 0.03 pa c,a for nests. / Master of Science / The bluehead chub is a keystone species, an ecosystem engineer that constructs mounded gravel nests for spawning. These nests benefit numerous other species within their habitat. The possibility of nest erosion is characterized in this study using existing sediment transport principles. Nest flow characteristics are measured using an acoustic Doppler velocimeter (ADV). ADVs are often the instrument of choice in measuring water velocity. The high resolution of these devices can capture turbulent flows well, however data collection often results in inclusion of erroneous spikes in velocity. These spikes represent points deemed impossible due to their sudden change in velocity magnitude. Spikes do not have a large effect on average velocities of ADV data, but can influence turbulence statistics that describe the turbulent fluctuations in flow velocities. To remove spikes, multiple methods incorporate different outlier detection principles. This study evaluates a popular method that employs a two-dimensional kernel density estimation (KDE) algorithm. A recent study suggested the possible simplification of this method to use a one-dimensional kernel density estimation instead. Both the 1D and 2D methods are evaluated in this study in how they filter ADV data and whether it results in a clean, improved velocity time series that would be expected in turbulent flows. A novel 1D KDE method was also developed as part of this study. The new method is found to produce the most reliable filtering. Despiked ADV data is used to characterize the hydraulics over bluehead chub nests sampled in Tom's Creek, Blacksburg, Virginia, USA. Hydraulics are evaluated to see if ambient flow upstream of a nest can characterize the flow characteristics over the peak of the nest. Shear stress amplification over the nest is used to find a critical threshold for nest erosion based on ambient flows. Stress amplification in the ambient flow to the peak over the nest is found to be a simple proportion, and amplification factor of 1.66. This means we expect shear stress over the peak of a chub nest to be 1.66 times greater than the ambient bed shear stress upstream of the nest. This amplification factor can be used with existing methods to calculate critical non- dimensional shear stress values, also known as the critical Shields stress. After accounting for the amplification factor of 1.66, a critical Shields of approximately 0.03 is found.

Swimming performance strongly influences fitness in aquatic organisms and is closely tied to external body morphology. Although this connection has been closely examined at the individual and species level, few studies have focused on this relationship as it pertains to functional group assemblages. Using functional groups based on similarities in habitat use and morphology, I tested the hypothesis that swimming performance can be reliably predicted by functional group composition. I measured swimming performance as burst speed using a simulated predator attack and as prolonged speed using a step-endurance test in a laboratory flume. I measured morphology using geometric morphometric techniques. A difference in swimming behavior in four of the seven species was observed in the step-endurance test. Benthic species exhibited bracing behavior as an alternative to body-caudal fin (BCF) propulsion in the prolonged speed trials. Swimming performance exhibited a weak relationship with functional groups based on habitat or morphology. Rather a species-based model was the best predictor of swimming performance. Although species exhibited variation in swimming performance, body size was the strongest predictor of absolute swimming performance across all models. Relative swimming performance (measured in body lengths/sec) was negatively related to body size. The results of this study suggest that functional groups are not always reliable predictors of performance and they necessitate empirical testing to validate their effectiveness. This study also provides critical swimming performance data for previously unstudied Great Basin fishes which could be valuable for predicting fish passage through culverts, weirs and fish ladders.

The population genetics of species occupying formerly glaciated regions are not only impacted by glacial retreat but also agricultural land use that is typical of such regions. Areas which have experienced glaciation often display a lowered amount of genetic variability and minimal population structure, and these effects become more predominant with increasing distance from a potential refugial population. Meanwhile, agricultural land use over the recent past has also been demonstrated to disrupt population structure distribution through disturbance regimes. The purpose of this study was to assess potential post-glacial and agricultural effects on populations of creek chub (Semotilus atromaculatus) in two agricultural watersheds that differ in the glacial history. The Saint Joseph River (SJR) watershed, Indiana and Michigan, USA was entirely glaciated during the last glacial maxima, while the Little Miami River (LMR) watershed in Ohio, USA, is situated on the boundary of the glacier. The degree of agricultural land use also varies between and within the two watersheds. Using eight microsatellite loci, 312 individuals were genotyped from 13 sites in SJR and 2,318 individuals from 29 sites in LMR. Measures of genetic differentiation showed that there was strong differentiation between watersheds. Analyses within watersheds recovered additional but weaker differentiation that was mostly associated with the geography of sub-watersheds and isolation by distance. Proximity to the glacial boundary appeared to play a minimal role in genetic differentiation and genetic variation. Differentiation among localities was not directly associated with the glacial boundary within LMR, and localities in this watershed had lower allelic richness and heterozygosity than those in the fully glaciated SJR. After accounting for the positive correlation of stream distance in LMR using partial Mantel test, both glacial history and agricultural land use were positively correlated with genetic differentiation. However, these predictor variables were also strongly correlated with one another which prevented disentangling the two potential effects. Within SJR, no 10 relationship of genetic differentiation with agricultural land use was recovered. My study shows that there is not a simple relationship between glacial history, contemporary land use, and genetic differentiation in creek chub. Rather, it appears that the patterns of genetic variation observed may be more closely linked to the dispersal behavior of creek chub within and among watersheds, and the history of effective population size within watersheds.

Niche separation may be the key to promoting the long-term coexistence of introduced and native species. Physical alterations to the environment (habitat manipulation) or re-introducing native species to former habitats can exploit the maladapted traits of introduced species to create a refuge for native species. No two species have identical niches because evolutionary constraints differ between species with different evolutionary histories. Our objectives were to determine if cold temperatures could promote coexistence between native least chub and introduced western mosquitofish. We used individual scale and population scale experiments to test four hypotheses: 1) colder temperatures would reduce the aggressive behavior and predatory effects of western mosquitofish on least chub, 2) colder temperatures would reduce the effect of western mosquitofish on the habitat use, activity, and feeding of least chub, 3) western mosquitofish would not be able to overwinter without warm refuges, and 4) western mosquitofish reproduction would be delayed or absent at colder temperatures, whereas colder temperatures would not inhibit least chub recruitment. At the individual scale cold temperatures reduced the aggression and predation of western mosquitofish on least chub. However at the population scale there was little recruitment in the cold treatment and juvenile least chub did not survive the winter in the cold treatment. Adult least chub successfully overwintered at freezing temperatures whereas western mosquitofish had no recruitment in the cold treatment during the summer and no western mosquitofish survived the winter. There is adequate niche separation among the adults to promote coexistence but the juveniles of both species require warm habitat in the spring and summer to survive freezing winter temperatures. Habitat manipulation may reduce the availability of warm winter refuges for western mosquitofish while leaving warm habitats during the spring for least chub spawning and recruitment. Transplanting least chub to former cold habitats could eliminate western mosquitofish because of niche separation between the species along a temperature gradient. We suggest that the niche separation hypothesis has general application for the restoration of a variety of threatened native species.