Systematics, Genomics, and Biogeography of Fungus–Photoautotroph Interactions in Lecanoromycetes and Eurotiomycetes

Abstract

Symbiosis is a ubiquitous phenomenon across the tree of life. In the fungal subphylum Pezizomycotina, symbiotic interactions with land plants, green algae, and cyanobacteria are ecologically diverse and have led to the proliferation of species. I address three main questions connected to Lecanoromycetes and Eurotiomycetes, sister classes that have taken dramatically different trajectories: Lecanoromycetes are almost all lichenized fungi, while Eurotiomycetes includes lifestyles as diverse as animal pathogens, plant mutualists, and rock-inhabiting extremophiles. (1) What is the species- level biodiversity of lichen-associated Trebouxia, and how do these species vary in their ecological interactions and environmental niches? (2) How do lichenized fungi and algae contribute to the biodiversity of southern Africa, and do they follow regional biogeographic patterns associated with vascular plants? (3) How are different trophic modes and lifestyles distributed in the phylogeny of Eurotiomycetes, and how do these lifestyles differ (or not) at a genomic level? In the first research chapter, I show that the distributions of Lecanoraceae fungi and their Trebouxia algal partners in Bolivia are structured by elevation. Maximum species turnover in the fungi and algae occur at different elevations, suggesting that the partners respond differently to change along the elevation gradient. I also contribute to the development of a phylogenetic classification for Trebouxia, recognizing several novel, putative species from Bolivia based on internal transcribed spacer (ITS) and rbcL data. In the second research chapter, I continue to develop the classification for Trebouxia using data from South Africa and Namibia. Ninenovel, putative species are proposed, and several putative species recognized in iv previous work are reassessed or rejected. I show that there is no evidence for the Greater Cape Floristic Region being a unique source for endemic Trebouxia species; conversely, there is evidence for extensive inter-biome sharing. In the third research chapter, I explore lichen species described by Nylander from South Africa in the 1860s. I show that the collector was likely Olivia Wolfenden Armstrong, that the collection locality is the Karkloof area, and that a species later described from the same region, Bacidia triphragmia (Stizenb.) Zahlbr., is a synonym of Nylander’s species Bacidia inconveniens (Nyl.) Zahlbr. The fourth research chapter continues to address the systematics of lichen- forming fungi in South Africa, focusing on the hyaline-spored species of Graphidaceae tribe Graphideae. Most South African collections from this group belong to pantropical species; an exception is the new species Allographa oldayana I. Medeiros, a putative endemic to forest fragments in eastern South Africa. I make the new combination Mangoldia bylii (Vain.) I. Medeiros and show that it is an earlier synonym for Mangoldia atronitens (A. W. Archer) Lücking et al. In the final research chapter, I obtain genomic and multilocus sequence data for endophytic, endolichenic, lichenicolous, lichenized, and bryophilous Eurotiomycetes and put these trophic modes in a phylogenetic context. There is no evidence for hybridization in the phylogeny of Phaeomoniellales, suggesting that difficulties inferring phylogenetic relationships among genera are likely due to incomplete lineage sorting. The new combination Knufia muscicola (Racov.) I. Medeiros & Greiff and the new genus Pseudoepibryon I. Medeiros & Greiff are proposed to partially resolve the polyphyly of Epibryon. Comparison of CAZyme and protease diversity does not show differences between endolichenic and lichenicolous Chaetothyriales.