| Summary: | In this dissertation, I explore the diversity of endophytic fungi associated with above-ground tissues of neotropical ferns, assess factors shaping their community structure in three forests, and explore the contributions of endophytes and related strains to our understanding of the diversity and ecology of a representative genus of Ascomycota. In Appendix A, I report a survey of endophytic fungi from seven species of ferns at La Selva, Costa Rica. Using both species-level and phylogenetic analyses, I compare culturable endophytes as a function of fern taxonomy, frond tissues (blades vs. stalks), habits (terrestrial vs. epiphytic), and vegetation types (arboretum vs. primary and secondary forest) during two consecutive years. Analysis of>500 strains provides a first taxonomic overview of fern endophytes at a community scale and reveals high diversity, host preference, and interannual variation in fungal assemblages. However, when variation due to host species is taken into account, community structure is similar among fern tissue types, habits, and sampling sites over a small spatial scale. In Appendix B, I expand my work to evaluate the abundance, species-level and phylogenetic diversity, and distributions of fern-affiliated endophytes in three neotropical forests (La Selva, Costa Rica; Barro Colorado Island, Panama; Los Tuxtlas, Mexico). My analysis of > 2000 isolates reveals that communities differ significantly among fern species within sites, and among ferns in different sites. Intersite differences in communities are correlated with geographic distance and environmental dissimilarity. My work suggests that extrapolative estimates of fungal diversity should take into account not just host species, but locality and environmental variation as well. In Appendix C I focus on a representative genus of Ascomycota (Lecythophora) to evaluate how multi-locus phylogenetic analyses of endophytes can detect new species. Lecythophora is a geographically widespread genus that includes opportunistic human pathogens, produces novel secondary metabolites, and consists presently of six described species. Multi-locus analysis of 33 newly collected strains suggested seven phylogenetic species that are new to science and highlighted their capacity to inhibit growth of two plant pathogenic fungi. This work shows how recognition of cryptic species even in well-characterized genera has major implications for estimating fungal biodiversity.
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