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A revolution in fungal systematics is underway due to the application of molecular phylogenetic analyses to previously intractable problems posed by unculturable fungi, unlinked lifecycle stages, and hidden diversity. Three chapters here detail how molecular phylogenetic analyses provided a taxonomic framework for early derived lineages of ascomycetes (Neolectales and Pezizales) upon which morphology could be re-examined for homology, linkage of lifecycle stages, and reconstruction of character states. Mitospores of fungi are rarely linked to meiospore stages in nature, unless they are temporally or spatially coordinated, or one form produces the other in culture. In the first chapter molecular phylogenetic analyses of ITS (a fungal barcode) and 28S rDNA are used to link mitotic sporemats that are produced on the soil surface with rarely cultured or unculturable ectomycorrhizal Pezizales. In this study, 48 OTUs representing six independent ectomycorrhizal lineages were delimited from 292 spore mats collected in Asia, Europe, South America, and North America. Most were truffle lineages, but one lineage included above ground cupuliform fungi, and one lineage had no detected meiospore stage. The discovery that a high diversity of mitospore-mat producing ectomycorrhizal Pezizales are common and widely distributed across the world implies that mitospores play an important role in the lifecycle of these organisms. Neolecta, the only fruit-body forming extant genus of the earliest derived lineage of ascomycetes, was previously determined to be phylogenetically related to non-ascoma forming Taphrinomycotina. The second chapter presents research on septal pore characters in Neolecta vitellina to investigate whether the ascoma in Neolecta is analogous or homologous to later derived lineages of ascoma forming Pezizomycotina. Two unique structures were associated with the septal pores in Neolecta: a vacuolar crystal that lodged within the septal pore of disrupted cells, and a membranous matrix that plugged the pores. The Neolecta crystal appears to be similar in function to the Woronin body of later derived lineages, but differs by the organelle in which it is formed, the numbers of crystals formed per organelle, and the association of vesicles with the crystal. Unlike Pezizomycete septal pore structures the membranous matrix of Neolecta septal pores is not confined to the septum. These two unique structures are presented as evidence of an independent evolution of the Neolecta ascoma. Truffles have evolved at least 16 times from cupuliform Pezizales. Previous phylogenetic analyses have inferred that reversals from truffles to cupuliform fruitbodies are unlikely. Chapter 3 details the phylogenetic analyses of multilocus alignments from world-wide collections of Pachyphloeus (truffles) and Scabropezia (cupuliform fungi). In these analyses, Scabropezia was inferred to be embedded within Pachyphloeus, and a truffle was reconstructed as the ancestral form of this lineage, perturbing the idea that cup fungi have not evolved from truffles. It is likely that taxa are missing from this study that could change these results. All described species in the lineage were transferred to Pachyphlodes to redress the illegitimacy of "Pachyphloeus." Eight lineages with 45 OTUs were delimited, expanding the diversity in this genus 3-fold. Spore wall development was useful for interpreting differences in spore ornamentation among the eight lineages.