Thesis (Ph.D.)--University of Wyoming, 2008. / Title from PDF title page (viewed on Dec. 4, 2009). Includes bibliographical references.

Thesis (M.S.)--Brigham Young University. Dept. of Integrative Biology, 2004. / Includes bibliographical references.

Three aspects of Xanthoparmelia cumberlandia and Xanthoparmelia coloradoënsis populations found at two elevations are explored: clustering of secondary chemicals and the resulting implications for taxonomic distinctions, the usefulness of thallus size as an indirect measure of sexual fecundity, and the frequency of sexual reproduction. First, we use clustering of 46 chemicals produced by X. cumberlandia and X. coloradoënsis to evaluate the adequacy of the current taxonomic distinction between them. Using principal components analysis and UPGMA, we find that the currently recognized species boundaries indicated by the presence of stictic acid in X. cumberlandia and salazinic acid in X. coloradoënsis are supported by distinct differences in their chemotypes (combinations of secondary chemicals). Norstictic acid, which the literature also associates with X. cumberlandia, is found frequently in both X. cumberlandia and X. coloradoënsis, and is not a good distinguishing characteristic. No chemical difference between sexually fecund and sterile individuals was found. Second, we test the claim that thallus size can be used as an indirect measure of sexual fecundity. By comparing the number of apothecia, the total area of the apothecia, and the presence or absence of apothecia with thallus area, we found positive correlations between these measures of sexual fecundity and thallus size which are statistically significant. However, the total variation explained by these predictors is limited, and is significantly affected by elevation and micro-environmental features such as proximity to trees. We conclude that size is not a reliable synonym for sexual fecundity in X. cumberlandia and X. coloradoënsis. Third, we make inferences concerning the frequency of sexual reproduction based on the frequency of sexual structures, rare chemicals, and unique chemotypes. We predicted that sexual reproduction would be more frequent at lower elevations, consistent with a common pattern found in plants and animals. The frequency of sexual structures indicates that sexual reproduction is more common at the lower elevation, while frequency of rare chemicals and chemotypes implies that outcrossing is more common at the upper elevation. Since these indicators lead to opposing conclusions, we encourage the use of molecular markers to estimate the frequency of outcrossing directly.

Usnea hirta and Xanthoparmelia cumberlandia are commonly used as bio-monitors of air quality. In order to more accurately and efficiently determine the distribution of these two sensitive indicator species, we have developed a probabilistic distribution map as a function of 9 macroclimatic and topographic variables for the White River National Forest, Colorado using Non-Parametric Multiplicative Regression (NPMR) analysis. Furthermore, we also developed a logistic regression (LR) model for X. cumberlandia in order to evaluate the strengths and limitations of the NPMR model. The best model for U. hirta included four variables - solar radiation, average monthly precipitation, average monthly minimum and maximum temperature (log β = 3.68). The presence rate for U. hirta based on field validated test sites was 45.5%, 65.4%, and 70.4% for low, medium, and high probability areas, respectively. The best model for X. cumberlandia generated by both NPMR and LR involved the same variables - solar radiation, average monthly maximum temperature, average monthly precipitation, and elevation as the best predictor variables (log β = 5.10). The occurrence rate for X. cumberlandia using the NPMR model was 32%, 44.4%, and 20% for the low, medium, and high probability areas respectively while the LR model had 26%, 50%, and 38% for low, medium and high probability areas respectively. Although the LR model predicted a smaller high probability area compared to the NPMR model there was substantial overlap between the two. The U. hirta model performed better than the X. cumberlandia model. The reduced performance of our model especially for X. cumberlandia may be due in part to the absence of field measured data in the development of the model. Our study also suggested that the northeast and western part of the forest should be preferentially considered for establishing future air quality bio-monitoring reference sites. Finally, in the future a well defined sampling design with sufficient sampling sites, field measured predictor variables, and microclimatic data should be used in the development of predictive models.

Accurate species delimitation has critical implications for ecological and conservation studies; and for understanding factors driving diversification. However, a growing body of evidence indicates that morphology-based species circumspection in lichenized ascomycetes often fails to accurately represent the number of fungal species. The use of molecular data in lichen systematics provides an important alternative to traditional morphological characters for identifying natural groups and assessing evolutionary histories in challenging lichen taxa. In this work, I examined two common lichen-forming genera in western North America, Rhizoplaca and Xanthoparmelia, as models for investigating character evolution, species delimitation in morphologically and chemically diverse species, and identification of lineages in the early stages of divergence. Phylogenetic hypotheses were reconstructed to assess character evolution using sequence data from four nuclear ribosomal markers and fragments from two nuclear loci. I applied a multifaceted approach to delimit species in Rhizoplaca and Xanthoparmelia by assembling multiple lines of evidence using DNA sequence data, and genealogical and population genetic analyses. I have found that traditionally circumscribed species are not supported by molecular data. For example, in Rhizoplaca previously unrecognized lineages were identified within what has thus far been considered a single species. In contrast, morphologically and chemically distinct species within Xanthoparmelia were not supported by molecular data. Distinct medullary chemistries, growth forms, and the production of vegetative diaspores appear to have evolved independently multiple times in Xanthoparmelia. This work clearly indicates that morphological and chemical characters do not always accurately reflect lichen species diversity within even the best known and studied genera. My study of the Rhizoplaca melanophthalma species complex demonstrates that the genus Rhizoplaca, as presently circumscribed, is more diverse in western North American than previously thought. I present these analyses as a working example of species delimitation in morphologically cryptic lichenized fungi. In Xanthoparmelia diagnostic morphological and chemical characters have evolved in a highly homoplasious manner. In contrast to other studies documenting previously undiscovered fungal lineages masked within lichen species circumscribed by traditional morphological and chemical characters, my work suggests that species diversity has been overestimated in the lichen genus Xanthoparmelia.