Human activities are increasing the size, frequency and severity of disturbance across earth’s ecosystems including deserts. Exotic annual grasses have altered fire regimes by increasing the size, frequency, and severity of fires in these systems. Invertebrates make up a large proportion of ecosystem diversity, provide a wide range of ecosystem functions, and are good indicators of ecosystem function and resilience. Ants are particularly good indicators of ecosystem stability. The ability of rodents to modify plant community structure post-fire, could result in rodent communities having important indirect effects on invertebrate communities. In chapter 1 we report changes in ant forager abundance and diversity with fire and rodent treatments over a three year period in the Great Basin. We found that while rodents had significant effects on the plant community in burned plots, this did not affect the ant community. Fire, however played a significant role in determining ant species richness and Shannon’s diversity index. Ant richness and diversity were reduced in burned areas compared to unburned areas. Total ant forager abundance was unaffected by fire, however, the abundance of the most common ant species, Pogonomyrmex occidentalis, increased in burned areas. The overall abundance of the other species was reduced in burned areas. We saw increases in the densities of P. occidentalis mounds in burned areas, but the average size of those discs decreased. The total area occupied by P. occidentalis mounds remained equal between burned and unburned plots. In chapter 2 we compare the abundances of different groups of invertebrates, as well as the abundances and diversity of the ant communities, between fire and rodent treatments. We then compared how those responses differed between sites in the Great Basin and Mojave deserts. In this study, we found that the abundances of most invertebrate groups remained unaffected by fire and rodent treatments. In the Great Basin, however, the abundance of flying-foragers was reduced in burned areas. At both locations, ant species richness and Shannon’s diversity were reduced in burned areas. Species richness and Shannon’s diversity were negatively correlated with invasive plant cover at both sites, and invasive plant cover was positively correlated with fire. The loss of diversity can spell losses in important ecosystem functions, and invasive grass fire cycles threaten to make these losses permanent.

Several restoration methods intended to increase the success of aerially‐seeded perennial grasses were assessed to determine their effects on cheatgrass metrics and soil nutrient bioavailabilities. These methods were: 1) imazapic herbicide application (140 g ai ∙ ha‐1, 210 g ai ∙ ha‐1, and no application [control]), 2) vegetation manipulation treatments (50% sagebrush overstory thinning, 100% sagebrush overstory thinning, sagebrush overstory and/or vegetative thatch burning, and no manipulation [control]), and 3) alternative seeding treatments (aerial seeding with raking, aerial seeding with activated carbon [AC] addition, aerial seeding with sucrose addition, and regular aerial seeding [control]). Treatments were arranged in 3‐way factorial designs, which allowed main effects and interactions between treatments to be assessed. Responses were followed for two growing seasons following treatment. Main effects of treatments and their interactions on cheatgrass metrics are described in Chapter 2. Herbicide reduced cheatgrass weights and tiller and spikelet numbers in 2009, but these variables were greater than in no‐herbicide plots in 2010. Burning decreased cheatgrass densities but increased weights and tiller and spikelet numbers in both years. One hundred percent sagebrush thinning resulted in greater cheatgrass weights and tiller and spikelet numbers in both years and greater densities in 2010. Sucrose addition decreased cheatgrass weights and tiller and spikelet numbers in 2009, but increased these variables in 2010. An interaction between AC and herbicide treatment was observed, with AC potentially sequestering and lessening the negative effect of herbicide on cheatgrass. Aerial seeding with raking and 50% sagebrush thinning treatments were not found to significantly affect cheatgrass either year. The effects of treatments (herbicide, 50% sagebrush thinning, aerial seeding on snow, and aerial seeding with raking treatments omitted) on soil nutrient availabilities are described in Chapter 3. We used ion exchange resin (IER) membrane probes to measure extractable quantities of 15 ions over three time periods following treatment applications. Burning resulted in short‐term increases in many soil nutrient availabilities, including nitrate (NO3 ‐), phosphate (H2PO4 ‐), and sulfate (SO4 2‐). Sucrose addition reduced availabilities of NO3 ‐ and H2PO4 ‐ during the first winter and growing season. No changes were detected with AC addition or 100% sagebrush thinning during any sampling time.

Cheatgrass (Bromus tectorum) is an invasive annual grass common in several semiarid plant communities in the western U.S. B. tectorum presence increases fire frequency and size, reducing species diversity, and leading to annual species-dominated systems with inconsistent livestock forage potential and degraded wildlife habitat value. Most efforts to manage B. tectorum-dominated rangelands have focused on controlling the plant itself rather than addressing the causes of vegetation change. An alternative approach, ecologically-based invasive plant management (EBIPM), identifies treatments that can alter factors associated with the causes of succession, leading to a more desirable vegetation state. This study utilized the EBIPM framework to design a large-scale demonstration project, which implemented a series of manipulation treatments (mowing, prescribed fire, imazapic herbicide, and seeding with perennial species) to suppress B. tectorum and promote desirable species. The treatments were implemented at two semiarid shrubland sites in northwestern Utah. Treatments were evaluated by measuring resident vegetation cover, density, aboveground biomass, and litter and soil seed banks. Herbicide was most effective in reducing B. tectorum cover, density, and biomass, while fire was effective in reducing seed density in the litter seed bank. Treatment interactions were rarely significant; however, by combining fire and herbicide, increased B. tectorum control was achieved. Seedlings of seeded perennial grasses emerged in all treatments; however, establishment by the end of the first growing season was greatest in treatments involving fire. The results of this study indicate that using a decision-making framework to select a series of treatments that alter the causes of succession can improve the management of B. tectroum-dominated rangelands.

This thesis includes two studies: The first examined patterns of neutral genetic diversity within Bromus tectorum L. across the IMW region, and uses patterns of microsatellite (SSR) genotype distribution to make inferences about the respective roles of adaptively significant genetic variation, adaptive phenotypic plasticity, and facultative outcrossing in the ongoing invasion and recent range expansion of B. tectorum. It has been previously demonstrated that, due to extremely low outcrossing rates, it is possible to characterize individual genotypes of this species using four SSR loci. We sampled 20 individuals from each of 96 B. tectorum populations (classified by region and habitat) from throughout the IMW and used these SSR markers to characterize each individual. We found 131 four-locus SSR genotypes; however, the 14 most common genotypes collectively accounted for 79.2% of the individuals sampled. Individuals with certain SSR genotypes sorted strongly into warm or salt desert habitats (stringent habitats) and flowered earlier than individuals with genotypes from more mesic habitats, providing evidence of adaptively significant genetic variation associated with these genotypes. Other SSR genotypes were found across a wide range of habitats though they tended to be less prevalent in stringent habitats, providing evidence that adaptive phenotypic plasticity may be important for the distribution of some common genotypes. We observed very few heterozygous individuals, consistent with the highly inbreeding reproductive strategy of B. tectorum. Because specialist genotypes dominating recently invaded areas within the IMW region contained unique alleles, they are not likely to have resulted from recombination, leading us to doubt the role of facultative outcrossing as a significant mechanism facilitating the current range expansion of B. tectorum in the IMW.Previous research investigating the population and ecological genetics of Bromus tectorum L. in the North American invaded range has relied on either allozyme or microsatellite (SSR) genetic analyses, both of which have proven to have shortcomings. In order to overcome the issues associated with these other marker types, in the second study of this thesis we developed single nucleotide polymorphism (SNP) markers for B. tectorum by 1) obtaining normalized cDNA, 2) sequencing normalized cDNA using 454 sequencing, 3) aligning resultant contigs and looking for SNPs, 4) designing assays for SNP validation and genotyping using KASPar, 5) converting working KASPar assays for use with the Fluidigm EP1 platform using the 96.96 Dynamic ArrayTM IFC. Sequencing resulted in 1258041 reads, which assembled into 65486 contigs (20782 large contigs exceeding 500 base pairs). Using selection criteria of at least 10x coverage and 30% of the minor allele, 3333 putative SNPs were identified. We developed KASP assays for 255 putative SNPs, which resulted in 101 working polymorphic assays. Ninety-six assays were then successfully converted for use with KASP on the Fluidigm EP1 genotyping platform using 96.96 dynamic arrays.

Observations of Bromus tectorum L. (cheatgrass or downy brome) monocultures have shown that populations are susceptible to stand die-off or replacement failures. Die-offs, where the seed bank from the previous year fails to emerge, occurs in cheatgrass stands and it is unclear the trigger or cause. The fungus Fusarium has been identified in plant and seed samples from die-offs and may drive die-off activity through pathogenicity. Die-off recovery may take several years but cheatgrass populations eventually reestablish. The purpose of our study was to determine whether Fusarium is a potential player in a die-off, and understand how die-offs recover after multiple years of stand failure. Our objectives were to determine: 1- litter and water effects on die-off activity; 2- if fungal pathogens, such as Fusarium, decrease the proportion of cheatgrass emergence in a die-off; and 3- whether direct or broadcast seeding, water, and litter treatments increase establishment in recovering die-offs. Litter absent plots had significantly (P < 0.0001 and P < 0.001) more emergence at 49.2% and 41% compared to litter present plots 21.3% and 23.7%. The litter absent plots significantly (P = 0.0003 and P = 0.001) increased survival (82% and 52%) compared to litter present plots (70% and 41%). Direct planted versus broadcast seeding had significantly (P < 0.0001) more emergence, 36% to 11.9%. The addition of Fusarium inoculum to field plots did not effectively replicate anticipated disease levels. The fungicide treatment did not have a significant influence at either site. The results from the study indicate that nothing inhibits cheatgrass from establishing following a persistent die-off disturbance. A unique window may be available for land managers to revegetate natives in invasive populations as large quantities of cheatgrass seeds fail to emerge during die-off events.

The genus Fusarium has a wide host range and causes many different forms of plant disease. These include seed rot and seedling blight diseases of cultivated plants. The Fusarium-caused diseases of wild plants are less well-known. In this study we examined Fusarium sp. n-caused disease development on non-dormant seeds of the important rangeland weed Bromus tectorum as part of broader studies of the phenomenon of stand failure or ‘die-off’ in this annual grass. We previously isolated an undescribed species in the Fusarium tricinctum species complex from die-off soils and showed that it is pathogenic on seeds. It can cause high mortality of non-dormant B. tectorum seeds, especially under conditions of water stress, but rarely attacks dormant seeds. In this study, we used scanning electron microscopy (SEM) to investigate the mode of attack used by this pathogen. Non-dormant B. tectorum seeds (i.e., florets containing caryopses) were inoculated with isolate Skull C1 macroconidia. Seeds were then exposed to water stress conditions (-1.5MPa) for 7 d, then transferred to free water. Time lapse SEM photographs of healthy vs. infected seeds revealed that hyphae under water stress conditions grew toward and culminated their attack at the abscission layer of the floret attachment scar. A prominent infection cushion, apparent macroscopically as a white tuft of mycelium at the radicle end of the seed, developed within 48 hours after inoculation. Seeds which lacked an infection cushion completed germination upon transfer to free water, whereas seeds with an infection cushion were almost always killed. In addition, hyphae on seeds that did not initiate germination lacked directional growth and did not develop the infection cushion. This strongly suggests that the fungal attack is triggered by seed exudates released through the floret attachment scar at the initiation of germination. Images of cross-sections of infected seeds showed that the fungal hyphae first penetrated the caryposis wall, then entered the embryo, and later ramified throughout the endosperm, completely destroying the seed.

Quantification of soilborne pathogen inoculum loads is important in both agricultural and wildland settings. Quantitative Polymerase Chain Reaction (qPCR) methods using SYBR Green chemistry have been shown to be useful for quantifying fungal inoculum loads in environmental samples. The purpose of this study was to develop a method to quantify fungal pathogen inoculum loads in soil seed banks using a qPCR method with SYBR Green chemistry. The invasive annual grass Bromus tectorum was chosen for this seed bank study. There were three objectives: 1) to design target-specific primers for three fungal pathogens known to be important in Bromus tectorum seed banks, 2) to develop a procedure for measuring inoculum loads in field samples, including optimization of qPCR standard curves and protocols, for these pathogens, and 3) to perform qPCR using this methodology on a representative set of field samples to quantify pathogen DNA in seed bank soil and surface litter. The three pathogens were chosen for quantification based on their hypothesized roles in Bromus tectorum stand failure: the seed pathogen Pyrenophora semeniperda, an undescribed species of Fusarium seed rot pathogen belonging to the F. tricinctum species group (FTSG), and the newly-described causal agent of bleach blonde syndrome (Clarireedia capillus-albis). Primers designed for each pathogen were shown to be target-specific in tests against each other and 12 other fungal species cultured from B. tectorum seed banks. Subsequently developed standard curves for each pathogen had R2 values > 0.98, efficiencies between 90 and 110 percent, and generally optimal dissociation curves. Inoculum loads were expressed for each pathogen as picograms of DNA per microliter of extracted soil or surface litter. Significant differences in measured inoculum loads were found between the targeted pathogens and between soil and litter samples for each pathogen. The data provided reinforces that the SYBR Green qPCR method provides a potentially useful tool for the study of field seed and seedling diseases across a wide spectrum of both wildland and agronomic applications.

Bromus tectorum and other annual brome grasses have invaded many ecosystems of the western United States, and because of an annual-grass influenced alteration of the natural fire cycle on arid western range lands near monocultures are created and conditions in which the native vegetation cannot compete are established. Each year thousands of hectares become near monocultures of annual brome grasses. Pyrenophora semeniperda, a generalist seed pathogen of annual grasses, shows major potential as a possible mycoherbicide that could help in reducing the monocultures created by annual grasses. The purpose of this research was to identify the requirements for isolating cultures of P. semeniperda, search for a hypervirulent strain, and evaluate its effect in the field. The techniques for isolating the fungus have evolved and become more efficient. The first two years of working with P. semeniperda resulted in 11 isolates. During the third year of this study, we developed a single spore isolation technique that resulted in 480 additional isolates. Virulence screening resulted in detection of a range of isolate ability to kill non-dormant B. tectorum seeds. Ninety-two isolates represented a range of virulence from 0-44%. The variation in virulence was expressed mostly within populations rather than between populations. Similarly, virulence varied significantly within Internal Transcribed Spacer (ITS) genotypes and habitats but not between them. When conidial inoculum was applied in the field there was no observed difference in disease incidence between different levels of inoculum. This is thought to have been due to applying the inoculum under conditions in which most in situ seeds were infected and killed by already high field inoculum loads. While additional field trials are needed to optimize the inoculum effectiveness, the overall results of this research provide a good foundation for using P. semeniperda as a biological control for seed banks of annual brome grasses.

The genus Psilochalcis, of the Family Chalcididae, was originally described in 1905 by Kieffer. Mainly considered an Old-World taxon, the first North American Psilochalcis were not identified until 1981 by Grissell and Schauff. Little is known about the species distributions, biologies and ecological relationships of these parasitic wasps. This dissertation describes research conducted in central Utah setting arrays of Malaise traps in 4 different habitat types common to the Great Basin at three separate locations. A result of this sampling revealed a high abundance of multiple species of Psilochalcis wasps, particularly from one location and two habitat types. Chapter 1 describes three new species of Psilochalcis wasps namely; P. adenticulata Petersen, P. minuta Petersen, and P. quadratis Petersen. A review of all North American Psilochalcis species explains their distribution in Utah and throughout the surrounding western United States. A taxonomic key for all North American Psilochalcis species is given. Chapter 2 examines the seasonal abundance of P. minuta and P. quadratis and their associations with two common Great Basin habitat types. Both species show their highest abundance from late June through early August. Their peak abundance is shown to change dependent on the environmental conditions of temperature and precipitation. Psilochalcis minuta is significantly associated with pinyon/juniper (Pinus edulis or P. monophylla and Juniperus osteosperma) and P. quadratis is significantly associated with cheatgrass (Bromus tectorum). Chapter 3 describes the building of species distribution models for P. minuta and P. quadratis using a maximum entropy (Maxent) approach. Ten environmental variables were used to predict areas of optimal suitable habitat for each species. Multiple predicted sites were field sampled to test each model's effectiveness. Psilochalcis minuta occurred at nearly 90% of predicted sites, and P. quadratis occurred at 50% of predicted sites. Both species occurred at some non-predicted sites in other habitat types. Model analyses and field-testing results show the P. minuta model to be reliable in predicting areas of probable species occurrence, while the P. quadratis model is much less reliable in doing so. Aspect and fire disturbance show the highest percent contribution to both species' models. Slight differences in variable percent contribution between models suggest these species have sympatric distributions. Soil and slope are more important predictors of optimal suitable habitat for each species. Maintaining integrity between model predictions and field testing gave insights into other factors contributing to probable occurrence of Psilochalcis species.

Following its introduction to North America in the late nineteenth century, Bromus tectorum L., an inbreeding invasive winter annual grass, has become dominant on millions of hectares of sagebrush steppe habitat throughout Intermountain Western North America. It appears that within the last 30-40 years, B. tectorum has expanded its range southward into the Mojave Desert and also into more climatically extreme salt desert environments. Previous research using microsatellite markers and experimental studies has suggested that lineages found in desert habitats are genetically distinct from those found in the sagebrush-steppe habitat and possess suites of traits that pre-adapt them to these environments. To provide additional support for our hypothesis that desert habitat-specific haplotypes dominate and are widely distributed across warm and salt desert habitats, we genotyped approximately 20 individuals from each of 39 B. tectorum populations from these habitats and adjacent sagebrush steppe habitats using 71 single nucleotide polymorphic (SNP) markers. Our data clearly demonstrate that populations throughout the Mojave Desert region, as well as in salt desert habitats further north, are dominated by a small number of closely related SNP haplotypes that belong to the desert clade. In contrast, populations from adjacent environments are largely dominated by haplotypes of the common clade, which is widely distributed throughout the North American sagebrush steppe. Populations across all habitats were usually dominated by 1-2 SNP haplotypes. This suggests that inbreeding B. tectorum lineages can often maintain their genetic integrity. It also explains the strong association between marker fingerprints and suites of adaptive traits in this species.