O'Donnell, Ryan2026-03-032026-03-03https://hdl.handle.net/1885/733807012The Orchidaceae is one of the most speciose flowering plant families on Earth, and questions surrounding the family's extraordinary diversification through time continue to captivate biologists. The family is renowned for its diversity of floral forms and intricate pollination systems, and for their obligate dependence on symbiotic associations with mycorrhizal fungi for seed germination. Australia plays host to some of the world's most unusual terrestrial orchids, many of which exhibit a remarkable degree of both above and below ground specificity with respect to their pollinator and fungal associates. The majority of studies into the Australian orchid flora and its associated funga have thus far been narrow in scope with a focus on either a macro- or microevolutionary scale. In this thesis, I studied the Australian terrestrial orchid flora and its associated funga as a unified system spanning from the macro to microevolutionary scale. Beginning at the macroevolutionary scale, I synthesised phylogenomic data with over 70 years of orchid mycorrhizal fungal research incorporating fungal sequences, morphology, and germination data to detangle recalcitrant evolutionary relationships within the terrestrial orchid tribe Diurideae. I uncovered an unprecedented degree of fungal niche specificity and demonstrated that fungal symbiont preferences in the Diurideae are phylogenetically structured and can be used to support certain topological hypotheses despite confounding evolutionary histories. At population scale, I focused on a species complex of sexually deceptive greenhood orchids (Pterostylis; Pterostylidinae) where cryptic species are likely, and performed a population genomic study to determine levels of genomic variation between putative species and whether there is support for existing species hypotheses. Genotyping-by-sequencing revealed the presence of discrete genetic clusters, providing molecular support for morphologically delimited taxa. In this chapter I also provide the first preliminary evidence in the literature for hybridisation between species of Pterostylis within a clade where pollination by sexual deception has been experimentally confirmed and is predicted to be the dominant mode of pollination. Moving to the fungal side of the orchid-mycorrhizal interaction, I present two studies with a close focus on one of the core orchid mycorrhizal fungal families: Ceratobasidiaceae (Agaricomycetes; Cantharellales). Firstly, I performed a taxonomic review of the various anamorph-teleomorph typified generic names within the Ceratobasidiaceae. Using publicly-available ex-type sequence data, I inferred a phylogeny which reiterated the paraphyly of several genera within the family and formalised the synonymisation of several genera under a unified Rhizoctonia. Finally, to investigate fungal species boundaries at the genome-scale, I sequenced several putative operational taxonomic units of Rhizoctonia known to associate with species of Pterostylis using long-read sequencing. I present 38 new high quality whole-genome assemblies of Rhizoctonia. Using these data, I found clear genomic divergence thresholds across the Ceratobasidiaceae, allowing us to describe at least six new species of Rhizoctonia. I show that divergence thresholds currently in use do not adequately represent the level of diversity within the family, and highlight the discovery of several lineages that are entirely new to science.en-AU202610.25911/XJRN-3G28