Phylogenomic Systematics of Lichenized Fungi at Multiple Taxonomic Levels

Lichens are one of the most cited examples of mutualistic symbiosis between fungi and photosynthetic green algae or cyanobacteria. The photosynthetic symbiont (photobiont) provides the fungal partner (mycobiont) with carbohydrates, whereas the mycobiont protects the photobiont in the so-called thallus. Lichenized fungi are ubiquitous and have an impressive diversity with nearly 20,000 described species. For over 200 years, beginning with Linnaeus, lichen taxonomist has been describing and classifying new species and higher-level groups. Taxonomic groups were delineated by observing unique sets of fixed morphological, chemical, and reproductive characteristics. Over the past few decades, there has been an increase in the use of molecular genetic data to understand the evolution of lichenized fungi. These studies that have assessed the taxonomic placement of lichens in the fungal kingdom, the delimitation of lichenized fungal species, and the genetic structure of their populations. The taxonomic value of morphological and chemical phenotypic characters for lichenized fungi are difficult to assess without other independent sources of data. Therefore, molecular data have provided a new line of evidence to critically evaluate the usefulness of morphological, chemical, and reproductive characters. Today lichenologists are using molecular data to test traditional hypotheses of homology based on phenotypes. Generally, the findings are that many traditional systematic delineations are incongruent with molecular concepts. The chapters in this dissertation use the latest DNA sequencing technologies and molecular analyses to understand the evolutionary relationships of lichenized fungi at different levels of taxonomy ranging from family, genus, species, to populations. There are two chapters that focus on the diversification of taxonomic groups above the species level, a chapter that focuses on population genetics, and another that focuses on the delimitation of species boundaries.