The Bonneville Power Administration (BPA) Fish and Wildlife Program mitigates for impacts of hydroelectric dams on ESA-listed salmon and steelhead populations in the Columbia River Basin (CRB). Considering the sizable investments in mitigation and the diversity of stream habitats within the CRB, there has been a pointed effort to develop and identify meaningful metrics relating to fish populations and trends in their habitat across the CRB. The Integrated Status and Effectiveness Monitoring Program (ISEMP) was developed in 2003 specifically for this purpose, and is tasked with developing and testing strategies for determining the status and trend of salmonid populations and their habitats in the CRB. This thesis was funded by the BPA, ISEMP, Eco Logical Research Inc., the Snake River Salmon Recovery Board, and the Intensively Monitored Watershed project in the Asotin Creek basin with the purpose of investigating the efficacy of foraging modeling as part of a large fish habitat monitoring program. The primary objectives were i) to assess a foraging model's ability to predict fish density in study sites involved in long-term monitoring and ii) to evaluate energetic implications of restoration design and progress after implementation using a foraging model. To assess the foraging model's ability to predict fish density (objective i), we collected topography, drift, temperature, discharge, and fish population information to support foraging modeling, and we simulated flow patterns, drift, foraging, swimming costs, carrying capacity, and density. We then compared observed and predicted densities in 22 study sites from the John Day and Asotin Creek watersheds: Linear regression between observed and predicted fish densities was significant (R2 = 0.61, p < 0.001). When assuming spatially uniform drift densities and small fish territories, carrying capacity predictions were related to the number of foraging locations simulated, suggesting the model is highly sensitive to territory size assumptions. To evaluate restoration design and monitor restoration progress (objective ii), we simulated foraging before restoration, after a virtual restoration (carried out using the restoration designs in a GIS environment), and again followinfg restoration implementation. We used raster differencing to compare the "before" results to the virtual restoration results and then the "before" results to the "after" results. Hydraulic and foraging models suggested: Mean net energy intake increased following both simulated and actual restoration. Restoration structures generally slowed water's progress through the study site or caused pooling, both resulting in an increase in energetically favorable areas. Generally, more areas shifted from another state to having an acceptable energy balance than to an unacceptable energy balance.

There is currently a decline in large, old trees within many ecosystems where they play important ecological and economic roles. One ecosystem suffering from this decline is the bushveld savanna of South Africa. One particularly important species in decline is the ecologically, economically, and culturally significant marula tree (Sclerocarya birrea subsp. caffra). This species’ decline is characterized by a steep drop in recruitment of seedlings into the population. Rodents are known to influence plant communities across many ecosystems through herbivory of adult plants as well as predation of seeds and seedlings. This research provides a record of rodent species present in the bushveld savanna ecosystem of Balule Nature Reserve where a decline in marula recruitment is taking place. Further, it offers a summary of morphological statistics and natural history traits for these rodents. Morphological statistics can be used for species identification. Reproductive status of individuals can inform researchers about reproductive phenology and how it may be affected by environmental conditions. Finally, trapping for this study took place during an historic regional drought. Trapping success was used to develop a limited window into how reduced precipitation affects rodent abundances. Morphological traits measured coincide with those available in the literature. Reproductive activity for males and females of one species, Namaqua rock mouse (Micaelamys namaquensis ), did not overlap completely, with females not being reproductively active while males were. Individuals captured and identified as chestnut climbing mice (Dendromus mystacalis) had statistically significantly longer tails and hind feet, and were heavier than reported in reference works.

Pathogenic fungi are increasingly associated with epidemics in wildlife populations and represent a significant threat to global biodiversity. Snake fungal disease is an emerging disease caused by the fungus, Ophidiomyces ophiodiicola, and appears to be widespread in the eastern United States. Yet an evaluation of field diagnostics, and an understanding of the population-level consequences of the disease, are lacking. First, I evaluated the use of clinical signs to predict the presence of O. ophiodiicola across season and snake habitat affiliation (aquatic or terrestrial) and I compared two sampling methods to see if collection method impacts PCR result. Overall, snakes with clinical signs had a higher probability of testing positive regardless of season or habitat association. However, terrestrial snakes had a lower overall probability of testing positive for O. ophiodiicola compared to aquatic snakes. I found no significant difference between sampling methods. Second, I used Passive Integrated Transponder (PIT) telemetry, and multistate capture-mark-recapture modelling to determine if SFD affects the short-term survival, movement, and behavior of wild snakes. I found no difference in short-term survival for snakes with SFD. Snakes with SFD spend more time surface-active and have lower permanent emigration and temporary immigration rates than snakes without SFD.

Rhinichthys osculus, the Speckled Dace, is one of the most ubiquitous fish in western North America. Within the Southern California region, the local taxon is known as the Santa Ana Speckled Dace. The purpose of this study was to characterize and identify polymorphic microsatellite markers for R. osculus in which twenty-three were identified through Illumina pair-end sequencing. Seven of these loci were then used to examine the patterns of genetic variation and population structure that occurred within and among the watersheds in the Southern California. The study also examined the regional relationships among Southern California, Central California and Owen’s River Valley. Analysis of the microsatellite data revealed highly significant moderate levels of population structure exist within the Southern California region (RST=0.160, p=0.001). This structure is best explained by watershed as well as isolation by distance (R2=.2286, p=0.010). Highly significant geographic structure also exists among the geographic regions of Southern California, Central Coast, and Owen’s River Valley regions (RST= 0.600, p-value=0.001) that are congruent with the regional differentiation elucidated by mtDNA sequence data. In both cases, the degree of population differentiation was correlated with isolation by distance. Utilizing this information we were able gain a better understanding of the evolutionary relationships among the Southern California populations of Santa Ana Speckled Dace. Within the Santa Ana Speckled Dace populations we examined four models to explain the geographic structure: watershed, mountain range, tributary, and isolation by distance. While all were significant, the tributary model exhibited the higher level of population structure (RST= 0.160, p-value=0.001) and a significant correlation was exhibited between geographic distance and population structure, suggesting isolation by distance may be playing a role. The results of the microsatellite analysis are congruent with an earlier broad scale analysis of mtDNA sequence data that suggests the Central California and the Owens Valley populations diverged from each other prior to the divergence of the Santa Ana Speckled Dace populations from the Colorado Basin populations, and that the Central Coast populations were not established as a result of a migration event from the Southern California populations, as was previously hypothesized. Primarily due to human activity, Santa Ana Speckled Dace habitat has become highly fragmented resulting in some populations becoming extirpated. We hope this study will guide the strategies for the conservation of the remaining populations of Santa Ana Speckled Dace and watershed management in Southern California.

‘Aigarchaeota’, a deeply branching lineage in the domain Archaea with no cultivated representatives, includes both thermophilic and hyperthermophilic microorganisms that reside in terrestrial and marine geothermal environments. The ‘Aigarchaeota’ consists of at least nine proposed genus-level groups that have been confirmed via 16S rRNA sequencing, with ‘Aigarchaeota’ Group 1 (AigG1) being the focus of this study. Based on cultivation-independent genomic data available from several AigG1 members in Great Boiling Spring (GBS), NV, and Yellowstone National Park, 22 different types of growth media were designed and tested for their ability to support growth of AigG1. One of these cultures, G1-10, was found to contain AigG1 at ~5% abundance, as well as other novel thermophilic microbial groups including a new species of the genus Pyrobaculum, members of the candidate phyla ‘Calescamentes’ and ‘Fervidibacteria’, and the novel archaeal lineage NAG1 (‘Geoarchaeota’). To attempt to obtain pure cultures of AigG1 and other novel thermophiles, a single-cell sorting system using an optical trap and a microfluidic device was constructed. The system was validated by sorting E. coli cells, which demonstrated that single, viable cells could be reliably obtained. Using this single cell sorting device on the G1-10 culture, a pure culture of a member of the genus Pyrobaculum was obtained, which was shown to represent a distinct species in this phylum by whole genome sequencing and in silico DNA-DNA hybridization. Additionally, a pure culture of the first representative of the candidate phylum ‘Fervidibacteria’ from an enrichment culture derived from G1-10. Additionally, to aid in morphology-based sorting of AigG1 and stable isotope labeling studies, fluorescence in situ hybridization (FISH) based on catalyzed reporter deposition (CARD-FISH) were developed and an AigG1-specific probe was tested. CARD-FISH was successfully used to detect AigG1 in both the G1-10 culture and in natural sediment samples from GBS. Stable isotope labeling incubations were performed with a variety of 13C-labeled substrates (bicarbonate, amino acids, sugars, and short chain fatty acids) on GBS sediments and G1-10 culture samples, and CARD-FISH was used to specifically detect AigG1 in the fixed samples. Nanometer-scale secondary-ion mass spectrometry (nano-SIMS) will then be used to determine whether AigG1 was capable of taking up the different carbon substrates tested. Overall, the results and accomplishments from this project and follow up nano-SIMS analysis will allow a better understanding of the metabolic potential of AigG1 and will aid future efforts to attempt to obtain pure cultures of this novel lineage.

Livestock grazing is a common and extensive land use practice in the United States occurring in a wide range of habitat types. As such, livestock grazing has the potential to alter ecosystem structure, function and community composition. The primary component (Chapter 1) of this thesis examined the effects of cattle grazing in a San Joaquin Valley grassland on two target taxa: reptiles and small mammals. The study took place on the Chimineas Unit of the Carrizo Ecological Reserve, San Luis Obispo County, California during Fall 2009 and Spring 2010. These taxa were sampled on matched pairs of two grazed and two ungrazed sites. Live trapping methods appropriate to sampling reptiles (coverboards and pit fall traps) and small mammals (Sherman live traps) were used to determine species richness and abundance of these taxa. Uta stansburiana (side-blotched lizard) abundances were greatest on Ungrazed1 (Fall: 1.75±0.49 captures/night, Spring: 3.58±0.35 captures/night). In addition, Chaetodipus californicus (Spiny pocket mouse) abundance was also greatest on Ungrazed1. Population estimates generated by Program CAPTURE suggest C. californicus could be 6.27 times more abundant on Ungrazed1 than Grazed1. However, sample size issues and site level effects confounded and made it difficult to determine significant differences between the grazed and ungrazed treatments for both reptile and small mammal taxa. Habitat structure at these sites was also evaluated including small mammal burrow abundance and vegetation structure. Again, differences between the grazed and ungrazed pasture could not be discerned because of site level effects occurring among matched pairs. As such, this thesis illustrates the difficulty in studying grazing and its potential effects on biotic systems because an array of variables can make unclear the differences between grazed and ungrazed areas. As a follow up study (Chapter 2) I used logistic regression to model U. stansburiana presence to examine possible sources of variation observed at trapping array locations utilized in the main study (Chapter 1). Shrubs exhibited a quasi-complete separation of data points and the three best models included: 1) Bare soil cover (AICc = 28.12), 2) Holes (AICc = 29.76), and 3) Bare soil cover + Holes (AICc = 29.90). Shrubs, bare soil cover and small mammal burrow density were all positively associated with U. stansburiana presence at array locations. Although species have general habitat requirements based upon their ecology and evolution, variations in habitat utilization exists depending upon the resources present at a specific location. Quantifying basic ecological information on a site specific basis is important to managing populations by identifying important resources and habitat components utilized by a given species on a given site.

While a significant degree of salinity tolerance has been observed in the bivalve mollusk species Corbicula fluminea, the physiological and behavioral responses to changes in salinity by these organisms are not completely understood. It was hypothesized that Corbicula would initially avoid any salinity stress behaviorally through valve closure, but would eventually have to open to dispel anaerobic waste products and deal with the salinity. To explore this, Corbicula were collected and put through a series of experiments at salinity exposures of 0, 2.5, and 5.0ppt, with tissue water content and hemolymph osmolality being measured. After an initial 96-hour exposure period, it was observed that the tissue water content ratio of clams in 2.5ppt and 5.0ppt water dropped below that of the control groups in 0ppt. After a 24-hour time course experiment, it was observed that this change in tissue water largely occurred within the first eight hours of exposure for the 2.5ppt and 5.0ppt groups. It was also noted that the hemolymph osmolality of both the 2.5ppt and 5.0ppt groups rose to match the osmolality of the water in roughly the same time span. The osmolality of the control group did not match the osmolality of the 0ppt water, but was held at a constant level above it. In a later experiment measuring the same variables for clams in 10.0ppt, it was found that the tissue water and osmolality did not begin to change significantly until after 12 hours. The findings suggest that Corbicula osmoregulate at salinities lower than 2.5ppt, but osmoconform in salinities above that threshold. Furthermore, it seems that the clams are able and willing to tolerate conformation at 2.5ppt and 5.0ppt, but that they are reluctant to conform in 10.0ppt, behaviorally avoiding exposure for as long as possible.

Accounts of species’ range shifts in response to climate change, most often as latitudinal shifts towards the poles or upslope shifts to higher elevations, are rapidly accumulating. These range shifts are often attributed to species ‘tracking’ their thermal niches as temperatures in their native ranges increase. Our objective was to estimate the degree to which climate change-driven shifts in water temperature may increase the exposure of West Virginia’s native freshwater fishes to mountaintop removal surface coal mining. Mid-century shifts in habitat suitability for nine non-game West Virginia fishes were projected via Maximum Entropy species distribution modeling, using a combination of physical habitat, historical climate conditions, and future climate data. Modeling projections for a high-emissions scenario (Representative Concentration Pathway 8.5) predict that habitat suitability will increase in high elevation streams for eight of nine species, with marginal increases in habitat suitability ranging from 46-418%. We conclude that many West Virginia fishes will be at risk of increased exposure to mountaintop removal surface coal mining if climate change continues at a rapid pace.

Environmental gradients structure ichthyofaunal communities longitudinally along river networks via the selective filtering of species’ traits. In many instances, these environmental influences have created distinct zones of co-occurring fish species. Zonation studies have most often been conducted with taxonomic data (species x site matrices), but the increasing availability of functional trait data creates an opportunity to build more rigorous understanding of species’ co-occurrence patterns. Notably, zonation studies that use taxonomic data may not reveal the same patterns as studies based on trait data. In this study, we tested for distinct ichthyofaunal zonation in James River Basin, VA using a combination of historical (1950-1987) and contemporary fish occurrence records (1986-2016) that were aggregated within 12-digit hydrologic units (HU). Zonation tests were performed separately for taxonomic data and functional trait data, using a combination of non-metric multidimensional scaling and k-means cluster analysis. We detected three distinct taxonomic zones and three functional trait zones within the James River Basin. In addition, through identifying that taxonomic dissimilarity between HUs was strongly correlated with functional dissimilarity, these zonation patterns were determined to not be significantly different.

A persistent and reliable future terrestrial carbon (C) sink will depend on how stable forest production is under more variable climate conditions. We examined how age, forest structure, and disturbance history relate to the interannual variability of above-ground wood net primary production (NPPw). Our site in northern Michigan spans two experimental forest chronosequences and three late successional stands; the chronosequences have distinct disturbance histories, originating following either clear cut harvesting (“Cut Only”) or clear cut harvesting and fire (“Cut and Burn”), and range from 21 to 108 years old. Annual NPPw was estimated using dendrochronology and site specific allometric equations. We used a portable canopy LiDAR (PCL) system to derive canopy rugosity, a measure of the variability and heterogeneity of vertical and horizontal leaf arrangement, to quantify plot level canopy complexity. Counter to our hypothesis, we found that NPPw stability was greatest in the most frequently disturbed, Cut and Burn stands and lowest in less recently disturbed, late successional forest communities. Opposing trends in chronosequence interannual variation of NPPw indicated that stand age and canopy complexity are not consistently related to production stability. Furthermore, sub-canopy leaf trait properties and breadth were not, as hypothesized, correlated with canopy complexity or NPPw stability. Our mixed findings suggest that multiple factors, including stand age and disturbance history, interact to influence NPPw stability, but also highlight an unexpected dichotomy in which disturbance legacies at our site negatively impact the long-term trajectory of annual forest NPPw, but enhance its interannual stability.