I quantified habitat selection for the endangered Zuni Bluehead Sucker Catostomus discobolus yarrowi and the Navajo Nation Genetic Subunit (NNGS) Bluehead Sucker Catostomus discobolus - a recent taxon described from genetic information. Both taxa are found in northern Arizona and New Mexico border regions. I examined fish [≥50 millimeters (mm) total length (TL)] selection of microhabitat conditions (i.e., water velocity, substrate size, overhead cover, water depth, instream cover, and mesohabitat conditions [i.e., pool, run riffle], during summer base flow conditions for NNGS Bluehead Suckers, and during both summer base flow and high spring flow conditions for Zuni Bluehead Suckers in six streams). Electrofishing, seining, and snorkeling were used to evaluate fish occupancy. From this information, I developed stream specific habitat suitability criteria (HSC) and then generalized HSC for each taxon, and tested transferability of the generalized HSC to individual streams. Zuni Bluehead Suckers and NNGS Bluehead Suckers occupied similar habitats: low velocity pools; sand, silt, and pebble substrate; high percent of instream cover; and water temperatures ranging from 2-21°C. However, Zuni Bluehead Suckers selected for low (0-25%) overhead cover where as NNGS Bluehead Sucker selected for high (0-75%) overhead cover. This was likely due to the source of instream cover–aquatic macrophytes that required sunlight in the Zuni Bluehead Sucker streams, and large woody debris falling from overhead branches in the NNGS Bluehead Sucker streams. Suggestions for managers includes maintaining existing cover or artificially construct additional instream cover; promote overhead cover (e.g., maintaining large trees along streams) and pool mesohabitats. In addition to this work I also tested the new method of environmental DNA (eDNA) to further help conservation efforts for these taxa. Environmental DNA has typically been used to detect invasive species in aquatic environments through water samples. I compared the efficacy of eDNA methodology to American Fisheries Society standard snorkeling surveys to detect presence of a rare fish species. My study site included three streams on the Navajo Nation in northern Arizona and northern New Mexico containing Navajo Nation Genetic Subunit Bluehead Sucker Catostomus discobolus and the Zuni Bluehead Sucker Catostomus discobolus yarrowi. To determine sample sites, I first divided entire wetted area of streams into 100-m consecutive reaches. I systematically selected 10 of those reaches for snorkel and eDNA surveys. Water samples were taken in 10-m sections within each 100-m reach, and fish presence via snorkeling was noted in each 10-m section as well. Water samples were collected at the downstream starting point of each reach, and continued upstream in each section 5 to 8 m ahead of the snorkeler. A qPCR was run on each individual water sample in quadruplicate to test for sucker presence or absence. I was able to positively detect both species with eDNA sampling techniques in two out of three streams. Snorkeling resulted in positive detections of both species in all three streams. In streams where fish were detected with eDNA sampling, snorkeling detected fishes at 11-29 sites per stream, where as eDNA detected fish at 3-12 sites per streams. My results suggested that AFS standard snorkeling was more effective at detecting target fish species than eDNA. To improve eDNA sampling, the amount of water collected and tested should be increased. Additionally, filtering water on site may improve eDNA techniques for detecting fish. Future research should focus on standardizing eDNA sampling to provide a widely operational sampling tool similar to electrofishing, netting, and hydroacoustics.

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.

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

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.

Genetic variation was examined in bluehead wrasse, Thalassoma bifasciatum, populations along the Florida Keys. Interpretion of mean heterozygosity (H), percent polymorphic loci per population (P), genetic similarity, and F and G statistics demonstrated a clear division of wrasse populations into "northern" and "southern" groups. Correlation and cluster analyses indicated the six reefs can be grouped in a similar fashion based on genetic and environmental data. The conclusion from this analysis of wrasse populations in the Florida Keys is that substantial population subdivision occurs in response to differing selective pressures created by heterogeneous environments.