Quinoa (Chenopodium quinoa Willd.) is a staple grain for the indigenous people of the Andean region of South America with excellent nutritional qualities, including protein content. The objective of this study is to report on the development of fluorescence-tagged simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) to (1) genetically characterize the inherent diversity of 152 accessions of C. quinoa; (2) determine to what degree the CIP-FAO collection represents the range of genetic diversity in quinoa; and (3) test four hypotheses regarding quinoa?s center of diversity, Highland and Lowland clustering patterns, origin of Lowland varieties, and the origin of domestication. Thirty-five SSR loci comprising 432 alleles ranging from 5 (QAAT10) to 28 (QAAT50) alleles per locus (mean=13) were used to survey the 152 accessions of quinoa from the USDA and CIP-FAO collections. Heterozygosity was detected in 14.25% of the accessions for SNP loci and in at least one locus for 51% of the accessions. Both UPGMA and PCA analyses partitioned the quinoa accessions into two main clusters. The first major cluster consisted of accessions from the Andean highlands of Peru, Bolivia, Ecuador, Argentina, and extreme northeastern Chile. The other main cluster contained accessions from both the Lowlands of Chile and those collected by Emigdio Ballón The CIP-FAO collection appears to give a good representation of quinoa's genetic diversity within these two main clusters. The significance of patterns of genetic diversity within C. quinoa is discussed.

Critical mule deer (Odocoileus hemionus) winter ranges in southeastern Utah dominated by Wyoming big sagebrush (Artemisia tridentata var. wyomingensis [Beetle and A. Young] Welsh) have developed dense cheatgrass (Bromus tectorum L.) understories. These communities are currently characterized by predominately mature to decadent stands of sagebrush with few perennial grasses and forbs. Sagebrush seedlings and perennial grasses compete for limited resources with annual grasses and forbs. To determine the affects of cheatgrass control on sagebrush growth and reproductive characteristics, imazapic (PLATEAU®, AC 263,222) herbicide was sprayed at 438.5 ml/ha with water and methylated seed oil during active fall growth of cheatgrass in 2002. Sagebrush growth and reproductive variables were measured on browsed and unbrowsed (caged) plants on sprayed and non-sprayed paired plots on 6 sites. Cheatgrass and other annual forb pretreatment cover was reduced from 23% to less than 3% the first year after the herbicide treatement and only increased to 4% the second year. Soil moisture on the treated plots was available at 15, 30, and 60 cm for several days to several weeks longer than on the control plots depending on the depth in the soil and year. Annual leader growth and flowering seedstalk length were similar on unbrowsed and browsed shrubs, but the number of seedstalks per plant was decreased by browsing. The number of sagebrush flowering seedstalks was significantly reduced by the herbicide the first year after the treatment, but recovered by the second year. The decrease in flowering seedstalks per sagebrush reduced the number of sagebrush seedlings observed the second year after the treatment (control = 81,800 seedlings/ha and treated = 16,700 seedlings/ha). Both seedstalk length (treated = 13.4 cm and control = 11.2 cm) and annual leader growth (treated = 6.2 cm and control = 5.3 cm) were greater on treated plots than control plots. Overall, imazapic can provide a window of cheatgrass and annual forb control to allow big sagebrush seedlings and perennial grasses and forbs to establish.

The Northern Goshawk has been a species of concern since its decline in the early 1990s, which has been attributed in part to loss of critical breeding and wintering habitat. Nest site selection of goshawks has been correlated with certain specific site characteristics including, but not limited to, forest species composition, forest stand size, diameter of nest tree, percent cover, tree height, site slope, and aspect. The goshawk holds the status of a Management Indicator Species (MIS) on all of the six national forests in Utah. This status requires annual monitoring to track goshawk numbers and to address any activities on the forests that may affect nest site activity. Findings from the annual nesting data showed that some territories have been more active than others. We summarized the data from the three national forests in southern Utah in order to understand differences in nesting habitat among the forests. We also analyzed the nesting habitat variables slope, elevation, and nest tree species statistically to determine if they could be used as predictors of nest activity. We found that slope and elevation were not good predictors while nest tree species was significant in its ability to predict nest activity. We concluded the nesting habitat variables we selected were insufficient in their ability to predict nest activity and other variables such as prey species availability, weather conditions in the spring, and forest cover type might be needed to create a model that more accurately predicts nest activity.

We describe a case study evaluating the ecological impact of Bromus tectorum L. (cheatgrass) invasion following fire disturbance and the effectiveness of revegetation in improving ecological integrity in a degraded semi-arid shrub steppe system. The effectiveness of rehabilitation efforts was assessed from measurements of arthropod richness, vegetation and arthropod community composition, and ground cover characteristics in three habitats: undisturbed, burned and weed-infested (B. tectorum), and burned and rehabilitated with native and non-native vegetation. Arthropods were collected in each habitat using pitfall traps. Differences in arthropod richness were compared using rarefaction curves. Non-metric multidimensional scaling, and non-parametric multivariate statistical procedures including analysis of similarity and similarity percentages routines were used to compare arthropod and vegetation community composition and ground cover characteristics between habitats. Arthropod communities in the rehabilitated habitat were distinct from and intermediate to those observed in the undisturbed and weed-infested habitats. Rehabilitation in this instance resulted in an improvement in ecological integrity and perhaps an intermediate step on the way complete restoration. Arthropod richness, arthropod and vegetation community composition, and ground cover characteristics were all useful indicators of ecological integrity, but returned slightly different results. Assessing multiple variables yielded the most complete understanding of the habitats studied.

Under Gause's principle two species cannot indefinitely occupy the same niche. The north and south arms of Great Salt Lake are separated by a rail causeway, resulting in salinity differences and color variation between the arms. Farmington Bay is also separated from the south arm by a vehicular causeway to Antelope Island. These causeways allow examination of competitive exclusion of cyanobacteria in the hypersaline environment of the Great Salt Lake. Cyanobacterial distributions partially map salinity, with Aphanothece halophytica proliferating in the north arm, and Nodularia spumigena in the south arm. I hypothesized that cyanobacterial species abundant north of the railway causeway are competitively excluded from the south by other species, and that cyanobacterial species that thrive and bloom south of the Antelope Island causeway cannot grow in the high salinity of the north. To test these hypotheses, 129 flasks of autoclaved water from the north and south sides of each causeway were inoculated with Great Salt Lake water samples from the north and south sides of the causeways. Four genera of cyanobacteria, Aphanothece, Oscillatoria, Phormidium, and Nodularia were identified and counted from the culture flasks using comparative differential interference contrast, fluorescence, and scanning electron microscopy. Counts of the cyanobacteria found in each flask were totaled and two way Analysis of Variance tests as well as exact tests were performed. Rankings of median abundances were also calculated. These data support the first hypothesis because Aphanothece halophytica was found in all inocula, but appears to be suppressed by the presence of Nodularia spumigena, which periodically blooms. The second hypothesis is also supported by the data because N. spumigena was found only in inocula from the less saline waters south of Antelope Island causeway, and apparently cannot survive the high saline waters north of the railway causeway.

The wild turkey is endemic to North America and has played a role in human cultures past and present. However, with the turkey's elusive behavior some aspects of its ecology are challenging to understand. Diet is one of these difficult aspects to study. The purpose of this study was to determine the diet selection of wild turkeys in central Utah using non invasive stable isotope technology. We hypothesize that turkey diet is highly specific, that consumption of specific plant species correlates with the needs of the individual turkey, and that stable isotope analysis will reveal patterns in annual dietary intake. Vegetative forage, turkey feces, and feather samples were collected from the Salt Creek area east of Mt. Nebo during 2007 and 2008. Feces samples were identified to bird sex and forage samples were identified to family or growth form (grass, forb, and shrub) when species could not be determined. Carbon isotope analysis of turkey feces and dietary forage using a mass spectrometer revealed that composition of turkey diet changed seasonally and yearly. Isotope analysis of dietary forage according to vegetative growth form revealed that turkey diet for the spring of 2007 contained approximately 46.0% grasses, 30.0% forbs, and 24.0% shrubs and trees. The summer diet for 2007 consisted of 39.0% grasses, 31.0% forbs, and 30.0% shrubs and trees. During spring 2008, grasses comprised 10.3% of the diet whereas forbs and tree/shrubs constituted 53.0% and 36.7%, respectively. Turkey summer diet for 2008 was found to consist of 13.1% grasses, 48.5% forbs, and 38.4% shrubs/trees. Isotope analysis of turkey feathers revealed no significant patterns in isotope signatures in relation to vegetation type and season of year. Stable isotope signatures resulting from fecal analysis reflect opportunistic foraging behavior as birds utilized a wide variety of forages throughout the year. Our findings suggest habitat structure and type play a more major role in wild turkey survival then food type. These findings also strengthen the need to rigorously evaluate turkey habitat prior to reintroduction with respect to vegetative composition and structure and their relationship with wild turkey behavior and life processes.

Various criteria or lines of evidence have been used to identify ancient Maya marketplaces, including location near trade routes, artifactual evidence of trade, open space adjacent to transportation routes, proximity to public structures, low platforms and rock alignments to denote market spaces, and regular patterns in soil and floor chemical concentrations. Seibal and Mayapán were important economic Maya polities controlling the trade routes at the apex of their civilizations. The objectives of these studies were to apply geochemical and geospatial analyses of the soils and floors from public plazas and household patios, to discover the anthropogenic chemical residues of phosphorus (P) and heavy metals associated with the trade of foodstuffs and workshop items that may have been marketed there. Public access, causeways, reservoirs and a pattern of high P and metal concentrations are consistent with marketing of organic foodstuffs and workshop items within suspected marketplaces of each site. In contrast, geochemical patterns of the soils and floors of household structures are consistent with ceremonial and household activities.

This thesis includes three studies. The first study examined how reductions in light availability and changes in soil chemistry that occur as conifers establish in aspen stands, differentially affects the regeneration success of aspen and conifers. We found that aspen were more sensitive to changes in light and soil then subalpine fir. For aspen, reduced light and conifer influenced soils significantly reduced height, biomass, photosynthesis and the production of secondary defense compounds. Subalpine fir seedlings were significantly reduced in photosynthesis, biomass and R:S under lower light conditions but showed no differences in physiology or growth when grown on the contrasting soil types. Subalpine fir seedlings were significantly reduced in photosynthesis, biomass and root:shoot ratio under lower light conditions but showed no differences in physiology or growth when grown on the contrasting soil types. Results from this study suggest that reduction in light and changes in soil chemistry associated with conifer succession place constraints on aspen growth and defense capacity, which may contribute to losses in aspen cover under longer disturbance return intervals. The second study looked at regeneration dynamics of aspen and conifers as forest stands transition from canopy gaps to aspen dominated canopies to conifer dominated canopies. We found that as overstory conifer density increases, aspen decrease in density, basal area, and seedling establishment. Conifers were shown to establish closer to aspen as the canopy increased in conifer density. As this proximity relationship extended into the canopy there is increased mortality in both aspen and subalpine fir, suggesting both facilitation and competition. Our third study looked at the physiological effects of smoke exposure on growth and primary and secondary metabolic responses of deciduous and conifer tree species. Twenty minutes of smoke exposure resulted in a greater than 50% reduction in photosynthetic capacity in five of the six species we examined. Impairment of photosynthesis in response to smoke was a function of reductions in stomatal conductance and biochemical limitations. In general, deciduous species showed greater sensitivity than conifer species. Smoke had no significant affect on growth or secondary defense compound production in any of the tree species examined.

We determined the diet contributions of grasses, forbs and shrubs for three herds of bighorn sheep along the Wasatch Front, Utah using stable isotope techniques and determined the electivity values for different forage species for four herds. Forbs were generally the most common forage eaten across all herds while shrubs were the least used forage resource. The Provo Peak and Mount Nebo herds used grasses, forbs and shrubs at proportions similar to other bighorn sheep populations across the west, while the Antelope Island herd used forbs at higher levels than any other local herd. Additionally, the herd on Antelope Island was analyzed to compare differential use by rams and ewes. Our results indicate that there was no significant difference in diet between sexes on Antelope Island. Bluebunch wheatgrass (Pseudoroegneria spicata) was a common species across all sites and was an important forage for all populations. Managers may consider these proportions when seeding in bighorn habitat improvement projects.

Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritionally value (high in protein and mineral content) and ability to thrive in harsh climates (drought, extreme elevations, etc.) make it an important regional food crop throughout the Andean region. The objectives of this study were to develop genetic markers and to quantify genetic diversity within cañahua. A set of 43 wild and cultivated cañahua genotypes and two related species (C. quinoa and C. petiolare) were evaluated for polymorphism using 192 microsatellite markers derived from random genomic sequences produced by 454 pyro-sequencing of cañahua genomic DNA. In addition, another and 424 C. quinoa based microsatellite markers were evaluate as potential cross-species marker loci. A total of 48 polymorphic microsatellite marker loci were identified which detected a total of 168 alleles with an average of 3.5 alleles per marker locus and an average heterozygosity value of 0.47. A cluster analysis, based on Nei genetic distance, grouped the cultivated cañahua into a single dominant branch clearly separated from wild cañahua genotypes and the outgroup species. Within the cultivated genotypes, two dominant subclades were present that were further partitioned by AMOVA analysis into five model-based clusters. Significant correlations were found between genetic distance and morphological traits. The isolation by distance test displayed no significant correlation between geographic collection origin and genotypic data, suggesting that cañahua populations have moved extensively, presumably via ancient food exchange strategies among native peoples of the Andean region. The molecular markers reported here are a significant resource for ongoing efforts to characterize the extensive Bolivian and Peruvian cañahua germplasm banks, including the development of core germplasm collections needed to support emerging breeding programs.