|dc.description.abstract||Due to its complicated taxonomy, the ecology and evolution of the lichen genus Usnea has been understudied by lichenologists in New Zealand and around the world. To address this, almost 450 specimens of Usnea were collected in this study from 42 different sites around the North and South Islands of New Zealand. Molecular data (ITS rDNA) were generated for both the mycobiont and photobiont symbionts using specific algal and fungal primers. For the first time, the phylogenetic positions of the specimens within the genus Usnea in New Zealand and their associated photobionts were studied using Bayesian phylogenetic analysis of the molecular data. The reliability of some of the most important phenotypic characters, which usually are used in specimen identification to species, were evaluated by mapping the characters onto the mycobiont phylogenetic tree. Patterns of codiversification within New Zealand Usnea were investigated by examining phylogenetic congruence for the mycobiont and photobiont symbionts using three independent, geographically-referenced molecular datasets, which varied in phylogenetic diversity and spatial extent. In vitro culture protocols for symbiont isolation and synthetic relichenisation were optimised for Usnea specimens in New Zealand and some of the culturable endolichenic microorganisms associated with these specimens were identified.
Algal and fungal ITS rDNA regions were successfully generated for both the mycobionts and photobionts from 367 samples. The Bayesian mycobiont and photobiont phylogenetic trees revealed the first view of the phylogenetic position of Usnea specimens in New Zealand and some within-genus groupings are proposed based on the results of sequence-similarity BLAST searches, morphologically identified specimens, and the available Usnea species ITS sequences in GenBank. All photobionts associated with Usnea were from the genus Trebouxia and their phylogenetic tree suggested the presence of many different species including Trebouxia jamesii, T. brindabellae, and T. australis. Analyses of phylogenetic congruence between the mycobiont and photobiont genetic distances revealed very strong patterns of codiversification exist for the genus Usnea lichen in New Zealand at three spatial scales, from within one kilometre to across New Zealand. There was, however, some variation in these codiversification patterns, which is likely to be driven by both intrinsic and extrinsic factors, such as the specificity of both partners towards each other, environmental conditions, and the availability of symbionts and their habitat preferences. In vitro protocols successfully produced axenic cultures of both the mycobionts and photobionts and provided an opportunity to compare the morphology and structure of both symbionts in their non-lichenised forms. These cultures of the Usnea mycobiont and the Trebouxia photobiont were used to successfully create a synthetic relichenisations, which had very different morphology compared to the parental thalli. Numerous algal, bacterial, and fungal endolichenic microorganisms living within Usnea thalli were cultured and identified. Of these, a relichenisation experiment showed that the alga Coccomyxa spp. is proposed to be a potential second photobiont associated with some Usnea mycobionts. The results of this thesis have improved our understanding of Usnea biology, phylogenetics and ecology and provide a foundation for further studies of this genus.||en