In recent years, the importance of sagebrush to shrub-steppe ecosystems and associated plant and animal species has been recognized. The historical removal of herbaceous species by excessive and uncontrolled livestock grazing on many of our sagebrush ecosystems has resulted in a stagnant state where dense, competitive stands of sagebrush prevent herbaceous species from recovering. Most early research on sagebrush control was directed toward eradication to increase herbaceous forage for livestock production, rather than sagebrush thinning to improve shrub vigor and understory production for wildlife habitat and community diversity. Mechanical treatments have the ability to retain shrub and herbaceous components, while improving diversity within degraded sagebrush communities. This study evaluated the effects of 6 mechanical treatments and revegetation of a Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis) community in northern Utah that were treated in the fall of 2001 and spring of 2002 (aerator only). Disking and imprinting killed 98% of the sagebrush and significantly (p < 0.05) lowered cover and density of sagebrush more than any other treatment. Disking and imprinting was the only mechanical treatment to reduce cover and density of residual understory species, but also to successfully establish seeded grasses. One-way Ely chaining, 1-way and 2-way pipe harrowing, and aerating in the fall and spring reduced sagebrush cover from greater than 20% to less than 5% and reduced density by about half. Two years after mechanical treatment surviving sagebrush had greater leader and seed stalk growth than untreated sagebrush. Choice of a mechanical treatment to increase and diversify the perennial herbaceous component and retain the shrub component of sagebrush communities depends on the amount of residual herbaceous species, as well as economics. Chaining is potentially most economical for diversifying communities with a residual herbaceous perennial component. It is uncertain whether successful revegetation from disking and imprinting was a result of significant reduction in sagebrush, residual perennial herbaceous species, or both. Response of sagebrush communities with a very limited perennial herbaceous understory needs to be tested to determine how much and what kind of mechanical reduction in sagebrush is needed for successful revegetation.

Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, whole- genome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-genome survey, WGS yields lower sequencing depth and sequencing of uninformative loci. Targeted sequencing utilizes the speed and low cost of NGS while providing deeper coverage for desired loci. This thesis applies targeted sequencing to the genomes of two different, non-model plants, Artemisia tridentate (sagebrush) and Lupinus luteus (yellow lupine). We first targeted the transcriptomes of three species of sagebrush (Artemisia) using RNA-seq. By targeting the transcriptome of sagebrush we have built a resource of transcripts previously unmatched in sagebrush and identify transcripts related to terpenes. Terpenes are of growing interest in sagebrush because of their ability to identify certain species of sagebrush and because they play a role in the feeding habits of the threatened sage-grouse. Lastly, using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. Second, we targeted the flanking loci of recognition sites of two endorestriction enzymes in genome of L. luteus genome through genotyping-by-sequencing (GBS). GBS of yellow lupine provided enough single-nucleotide polymorphic loci for the construction of a genetic map of yellow lupine. Additionally we compare GBS strategies for plant species without a reference genome sequence.

Three predominant and economically important shrubs of the sagebrush-grass range community in Utah, namely big sagebrush (Artemisia tridentata Nutt.), rubber rabbitbrush (Chrysothamnus nauseosus (Pall.) Britt.), antelope bitterbrush (Purshia tridentata (Pursh) DC), and a widely re-seeded range grass, crested wheatgrass (Agropyron cristatum (L.) Gaertn.) were sampled during the summers of 1966 and 1967, and yielded twenty species of thrips. Three species (Anaphothrips tricolor Moulton, Chirothrips aculeatus Bagnall, Chirothrips simplex Hood) were new distributional records for Utah. Seven species (Frankliniella n. sp. #1, Frankliniella n. sp. #2, Haplothrips n. sp., Leptothrips n. sp., Oedaleothrips n. sp., Sericothrips n. sp. #1, Sericothrips n. sp. #2) were undescribed. Six species (Anaphothrips zeae (Moulton), Aptinothrips rufus (Gmelin), Chirothrips aculeatus Bagnall, Frankliniella minuta Moulton, Frankliniella occidentalis (Pergande), Thrips tabaci (Lindeman) had previously been reported as injurious to various range and agricultural hosts. The remaining species included: Aeolothrips duvali Moulton, Aeolothrips fuscus Watson, Aptinothrips rufus stylifera Trybom, Haplothrips sonorensis Stannard, and Rhopalandrothrips corni Moulton. Host preference, habitat preferences, and peaks in seasonal abundance were determined for each thrips whenever possible.

Greater sage-grouse (Centrocercus urophasianus; hereafter, sage-grouse) are a species of conservation concern in the rangelands of western North America due to their dramatic decline over the last half century. Effective conservation and management of sensitive species requires an understanding of how species respond to management actions. We examined two aspects of the reproductive phases of sage-grouse: nest predation, and habitat selection by female sage-grouse with chicks. In Chapter 1, we developed resource selection functions to assess the influence of mechanical treatments of mountain big sagebrush (Artemisia tridentata vaseyana) on habitat selection by greater sage-grouse with chicks. Post-treatment sage-grouse showed stronger selection for treatments and treatment edges than did pre-treatment sage-grouse. This altered pattern of selection by sage-grouse with broods suggests mechanical treatments may be a suitable way to increase use of mountain big sagebrush during the brooding period. In Chapter 2, we assessed the effect of habitat edges on nest predation of sage-grouse. The "edge effect" hypothesis states that habitat edges are associated with reduced nest success for birds. We tested the edge effect hypothesis using 155 nest locations from 114 sage-grouse. We derived edge metrics for 11 habitat cover types to determine which variables may have affected nest predation. We found support for the edge effect hypothesis in that nest predation increased with increasing edge density of paved roads. We provide evidence that the edge effect hypothesis may apply to greater sage-grouse and their habitats. Based on our results, we recommend minimizing disturbances that fragment critical nesting habitat of greater sage-grouse.

Habitat selection has long been viewed as a multi-scale process. Observed species responses to resource gradients are influenced by variation at the scale of the individual, population, metapopulation, and geographic range. Understanding how species interact with habitat at multiple levels presents a complete picture of an organism and is necessary for conservation of endangered species. The main goal of this dissertation is to evaluate distribution, relative abundance, and habitat selection of a rare species, the pygmy rabbit Brachylagus idahoensis, at multiple scales in order to improve management and conservation for this species. At the broadest scale, pygmy rabbit occurrence and relative abundance were modeled in the Duck Creek allotment of northern Utah using a hierarchical spatial model. Pygmy rabbits are not easily observable, and the model used two levels of indirect detection to make statistically rigorous spatial predictions. We found that the model predicted the general pattern of rabbit occurrence and abundance within the study area, and that there was spatial heterogeneity in the probability of pygmy rabbit occurrence within a study domain that was known to be occupied. The resulting model framework could be used to develop a long-term monitoring program for pygmy rabbits and other species for which hierarchically nested levels of indirect observation are collected. The mid-scale analysis evaluated pygmy rabbit home range placement and movement with respect to sagebrush removal treatments using null models based on an optimal central place foraging behavior. While placement of home-range centers did not appear to be affected by the treatments, within-home range movements were farther from treatments than expected by the null models for two rabbits (of eight), and rabbits that approached treatment edges were less likely to enter treatments than expected by chance. Rabbits are not extirpated from sites that have been treated, but the observed reluctance to enter treated patches calls for caution when conducting sagebrush removal treatments near occupied pygmy rabbit burrows. At the finest level of resolution, the spatial ecology of pygmy rabbit use of burrows was evaluated. Both the placement of burrows in general and pygmy rabbit use of burrows were clustered. While the habitat gradients experienced by each of the rabbits evaluated affected the modeled habitat selection responses, some generalities were observed. Selection of high cover suggests that pygmy rabbit use of burrows may be linked to predator avoidance behavior. Additionally, pygmy rabbit use of clustered burrows affects management actions including: habitat modeling, monitoring, and species introduction. Explicit attention to resource distribution will improve efforts to predict species responses to management actions.

Disturbances such as fire and grazing can degrade landscapes, but they can also rejuvenate them. I evaluated: 1) the practicality of strategically timed (fall), high intensity browsing of sagebrush (Artemisia tridentata ssp. tridentata, ssp. wyomingensis) by cattle; 2) the foraging behavior and body weights of cattle with varying levels of experience browsing sagebrush; and 3) the ensuing responses of grasses, forbs, and sagebrush to cattle grazing. In spatially and temporally replicated trials from 2007 to 2009, fall grazing by cattle reduced the abundance of sagebrush and promoted production of grasses and forbs. The cattle used in these trials were challenged to learn to eat sagebrush in the unfamiliar circumstance of confinement in small pastures. Throughout the trials from 2007 to 2009, pregnant cows with calves (2007), bred yearling heifers (2008), and first-calf heifer/calf pairs (2009) supplemented with protein and energy – to mitigate the effects of terpenes in big sagebrush – learned to select sagebrush as a significant portion of their diet. In virtually every case, experienced animals consistently used more sagebrush and lost less weight, or actually gained more weight, than naive animals in 2008 and 2009. My research suggests grazing by cattle during fall can be effective, biologically and economically, and can lead to habitat renovation and resilience. Moreover, grazing can create locally adapted systems in ways that landscape manipulations with chemical and mechanical treatments and prescribed fire cannot. These “technological fixes” are increasingly impractical due to environmental concerns, the high costs of fossil fuels, and the need to repeat outcome-based treatments rather than incorporating process-based approaches into managing landscapes. Rather than attempting to convert sagebrush steppe landscapes to grass at extravagant costs, as we have done historically, we must now consider ways to create locally adapted herds of livestock and complementary management practices to ensure long-term health of sagebrush steppe. As many ranchers already feed hay to cows during winter, using sagebrush steppe vegetation as an additional forage resource would allow ranchers to feed roughly half the hay, which would greatly reduce winter feed costs. In addition to financial savings in hay, the secondary benefits from improving sagebrush steppe condition and productivity would result in habitat improvements for both livestock and wildlife.

Crested wheatgrass (Agropyron cristatum [L.] Gaertn.) is one of the most commonly seeded grass species in the western United States and dominates thousands of hectares in the Great Basin. Although many degraded Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis) plant communities have been seeded with crested wheatgrass, successional pathways, influence of soil attributes, and cultivation history on the vegetation of these communities have not been fully characterized. I sought to identify community phases, vegetative differences, and soil attributes that explain variation among 35 Wyoming big sagebrush communities historically seeded with crested wheatgrass. All communities were more than 30 years old and had not experienced fire, or received subsequent chemical or mechanical treatments following their original seeding. Species richness, diversity, vegetation cover, and soil samples were measured in four 20 x 5 m intensive Modified Whittaker plots per community. Hierarchical clustering and principal component analysis of three indicator species (crested wheatgrass, Sandberg bluegrass, and Wyoming big sagebrush) identified four distinct community phases. Community phase 1 was dominated by crested wheatgrass and had the lowest species richness and cover of big sagebrush. Phases 2 and 3 had the highest species richness and cover of native species. Phase 4 was dominated by big sagebrush and had the lowest cover of crested wheatgrass. Community phases differed significantly for soil texture, soil nitrogen, and ground cover characteristics. Bare soil was almost double on loam-textured soils and rock cover was higher on clay loam texture soils (P < 0.05) as well as native plant cover. Communities previously cropped occurred on more coarse-textured soils and had 6-fold lower native species cover and double exotic herbaceous and crested wheatgrass cover. Cropping occurred on favorable, low rock, fine-texture soils, the same soils that favor crested wheatgrass production and reduce resilience of native plant composition. Delineation of community phases provided a new, empirically based state-and-transition model, while the characterization of soil attributes and disturbance history provided information about feedback mechanisms influencing dominant species that delineate community phases and effect community structure. This information can be used to assist in the development of management strategies in crested wheatgrass seeded communities.

This study consisted of two research projects in the Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis (Beetle & A. Young) S.L. Welsh) alliance, the most extensive of the big sagebrush complex in the Intermountain West. In the first project, we intensively sampled 107 relatively undisturbed, late seral Wyoming big sagebrush sites across the High Desert, Humboldt, and western Snake River Ecological Provinces to investigate vegetation heterogeneity and the relationship of environmental factors with vegetation characteristics. Vegetation characteristics were highly variable across the region. Perennial grass and total herbaceous cover varied more than six and sevenfold, respectively between minimum and maximum values. Sagebrush cover averaged 12%, but ranged between 3 and 25%. With the exception of perennial grass cover (p<0.0001, r²=0.52), limited variability in other vegetation characteristics was explained by environmental variables. In the second project, we investigated the functional role of Wyoming big sagebrush by using undisturbed and sagebrush removed (with burning) treatments and comparing vegetation and microsite characteristics under (subcanopy) to between sagebrush canopy (interspace) zones. Wyoming big sagebrush influenced associated vegetation and microsites. On sites receiving high incidental radiation, perennial grass and total herbaceous cover and density were greater in the subcanopy than interspace zones (p<0.05). On north aspects, these differences were not as pronounced suggesting sagebrush's influence on associated vegetation is site dependent. Temperature extremes were mediated and soil water content was greater in the subcanopy than interspace zones during the growing season. Results indicated that the subcanopy zone can be a more favorable environment to herbaceous vegetation than the interspace zone. Wyoming big sagebrush is important to community resource capture and use. Plots with sagebrush had greater soil water content at the start of the growing season and produced more total biomass compared to where sagebrush had been removed in both post-fire years (p<0.05). However, higher Thurber's needlegrass photosynthetic rates and greater herbaceous cover and production where sagebrush had been removed suggested that more resources were available to herbaceous vegetation in the absence of sagebrush. / Graduation date: 2006

Land-use legacies can affect landscapes for decades to millennia. A long history of shrub management exists in the sagebrush steppe of the Intermountain West where shrub-removal treatments, a type of managed disturbance, have been implemented for over 50 years to reduce sagebrush cover. The assumption behind managed disturbances is that they will increase forage for domestic livestock and improve wildlife habitat. However, the long-term effects of managed disturbance on plant community composition and diversity are not well understood. We investigated the legacy effects of three common types of managed disturbance (chemical, fire, and mechanical treatments) on plant community diversity and composition. We also examined sagebrush steppe resilience to managed disturbance. Based on management assumptions and resilience theory, we expected within-state phase shifts characterized by an initial reduction in biodiversity followed by a return to prior state conditions. We also expected changes in species proportions, characteristic of within-state shifts in state-and-transition models. We also expected an increase in non-native contribution to overall diversity. We found that plant communities experienced a fundamental shift in composition following disturbance, and responded in a flat linear fashion, giving no indication of return to prior community composition or diversity. As expected, we found post-disturbance increases in the number of non-native grass species present. However, native forb species made the largest contribution to altered diversity. Disturbance modified functional group composition, so contrary to our expectations, within-state changes did not occur as a result of disturbance. Our results indicated that sagebrush steppe plant communities are not resilient to chemical, fire, and mechanical treatments, and subsequent to managed disturbance, community composition tips over a threshold into an alternate stable state.

This study examined activity patterns and habitat use of pygmy rabbits (Brachylagus idahoensis) in mechanically treated and untreated areas in south-central Utah 2005-2008. We monitored fecal pellet plots in continuous sagebrush habitat as well as along treatment edges to record deposition and leporid presence over timed periods. Pygmy rabbit use of big sagebrush was higher than black-tailed jackrabbits (Lepus californicus) and mountain cottontail rabbits (Sylvilagus nuttallii ) (P< 0.01) relative to treated areas (P <0.01). We also compared pygmy rabbit use of areas with continuous sagebrush to residual sagebrush in a sample of mechanically treated areas. Our results suggest a treatment effect with higher (P <0.01) average counts of pygmy rabbit pellets in areas with continuous sagebrush compared to sagebrush strips and islands within treated areas. Before the big sagebrush biotype inhabited by pygmy rabbits is treated to reduce the occurrence and dominance of big sagebrush, we recommend managers consider two options. The first is no treatment, thus preserving, as is, the critical habitat of the pygmy rabbit and other sympatric big sagebrush obligate species of wildlife. The second option cautiously introduces the first prescription of habitat treatment ever recommended in relationship to the pygmy rabbit. This prescription includes recommended widths of the treated areas, seed mixes, widths of the preserved intact big sagebrush habitat for pygmy rabbits as well as suggested grazing systems for domestic livestock. Activity patterns of pygmy rabbits at their burrow were documented through the use of remote cameras. Photographs were analyzed for temporal and seasonal patterns of activity. Our results suggested that time of day was important in the activity level of pygmy rabbits while season was not. Pygmy rabbits were active during all time periods of the day but the greatest levels of activity occurred at night. Numerous other wildlife species were recorded by our remote cameras including other species of leporids, birds, rodents, reptiles and terrestrial predators.