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

Pendent Usnea species were collected in western Oregon and examined. Character states, such as cortex-medulla-axis ratio; fibril length; papilla diameter; branching patterns; and presence or absence of fibrils, papillae, soredia, isidia; plus chemistry, were recorded and analyzed by inspection for differences. Historical names were researched in the literature. A comparison was made between species concepts used in these accounts, with many conflicting concepts encountered. Selected morphological characters were examined by scanning electron microscope, or dissecting microscope, described, and illustrated. The characters reviewed included articulate fissures; isidia and soredia; cortex-medulla-axis ratio; papillae; and foveate pits. Species determinations were made for field collections. Names were found for all specimens inspected without introducing new names at this time. Eight pendent species were found in western Oregon; they are Usnea cavernosa, Usnea ceratina, Usnea fillpendula, Usnea hesperina subsp. liturata, Usnea inflata, Usnea leucosticta, Usnea longissima, and Usnea merrillii. A practical key to taxa with descriptions is provided and geographic distributions are recorded in tables and maps. / Graduation date: 1995

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.

This thesis deals with the phylogeny of the lichen genus Usnea (Parmeliaceae, Ascomycetes). The relationships and the morphological variation among Usnea species has been studied, as well as the relationship of Usnea to allied genera. Two species, U. florida and U. subfloridana, which earlier were regarded to form two separate species have been synonymized. In an analysis based on sequence data these two taxa formed a monophyletic group of intermixed specimens. Usnea florida and U. subfloridana have earlier been regarded to form a species pair, but the species pairs concept cannot be applied in this case. The morphological characters traditionally used for species recognition of a number of European Usnea species have been analyzed regarding their reliability. The evolution and distribution of the morphological characters was studied in relation to a phylogeny based on sequence data. Most characters proved to be homoplastic in relation to the phylogeny. Few characters were consistent in a clade, and the same character could be inconsistent in another clade. Therefore a combination of several characters is recommended for species recognition. The relationship of Neuropogon to Usnea was investigated based on sequence data. Neuropogon showed to be closely related to Usnea subg. Usnea. The subgenera Eumitria and Dolichousnea formed the sister group to the clade comprising subg. Usnea and Neuropogon. Usnea is paraphyletic in this investigation. Eumitria is treated as a genus and the subgenus Dolichousnea is elevated to generic rank. The position of Usnea, Neuropogon, Eumitria, and Dolichousnea in the family Parmeliaceae was investigated based on a phylogeny obtained by sequence data. Protousnea probably forms the sister group to the clade of Usnea, Neuropogon, Eumitria, and Dolichousnea. Several monophyletic groups in the family Parmeliaceae were identified.

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.