Abstract
Our understanding of the ecological role of the fungal kingdom is constrained by a lack of description of most fungal species. In Aotearoa New Zealand, it is estimated that the conventional approach of taxonomic descriptions based on sporocarps has described less than a third of the actual fungal species present. Globally, this number is far more drastic with less than a tenth of the estimated fungal species having been described. As conventional approaches fail to provide an efficient means with which to describe global fungal species diversity, many researchers have turned to DNA-based methods instead. DNA-based methods have been found to be more efficacious at showing population species diversity, and at determining species presence and prevalence. Environmental
DNA metabarcoding is one such set of methods that makes use of DNA extracted from environmental samples (eDNA), and next generation sequencing technologies, to identify a far greater proportion of the fungal species present in a sampled region than traditional methods.
This thesis aimed to use eDNA to gain a broad overview of genus Cortinarius from Te Wai Pounamu / The South Island of Aotearoa New Zealand, estimating the total amount of species diversity present whilst also identifying the described and undescribed species that exist in the region. This thesis makes use of a large eDNA sequence dataset, extracted from hyphal ingrowth bags and root tips, of six ectomycorrhizal fungal host species’ across Te Wai Pounamu / The South Island of Aotearoa New Zealand; Nothofagus menziesii, Nothofagus fusca, Nothofagus truncata, Nothofagus solandri, Nothofagus cliffortioides, and Leptosporum scoparium. Maximum likelihood phylogenies
and phylogenetic species concepts are combined with clustering approaches and analysis of co-occurrence patterns with the LULU algorithm to identify described species and prospective phylogenetic species: genetically concordant groups that are likely to represent undescribed species. These prospective phylogenetic species will operate as intermediary identifiers to allow for cross contextual discussion of undescribed Cortinarius species until physical specimens are discovered to allow for a formal description.
As well as the prospective phylogenetic species identified in this study, an analysis of specimen collections and scientific literature was also completed, to estimate the total number of Cortinarius species described from Aotearoa New Zealand. This analysis showed that 204 formally described species of Cortinarius are present in Aotearoa New Zealand.
In total, 636 species were detected in this study, comprising of 129 described species and 507 prospective phylogenetic species; 79.7% of the species identified were undescribed. Through analysis of the relationship between the number of species identified and the sampling effort, it is predicted that a further 80±16 species are present in the region that were not observed by this survey.
Estimations of species ranges are shown for all species and specimen collection data is combined in these for described species for which that information was easily available. This thesis will act as a foundation upon which a more efficient means of species identification will be built.