The aim of my thesis is to contribute to our understanding of intraspecific variation in fungi through the study of five Pleurotus species in Aotearoa New Zealand, exploring phenotypic and genotypic variation by applying methodology spanning systematics, ecology, biology, genomics, conservation, and food science. Intraspecific variation drives evolution, breeding, and food production practices, with implications for conservation, pathogenicity, biotechnology, and agriculture. Although well-studied in animals and plants, few mycological studies have focused directly on intraspecific variation, despite its growing recognition in the field. Edible oyster mushrooms (Pleurotus) are ideal model organisms because they experience natural selection in the wild and artificial selection in cultivation.

As a foundation to assess phenotypic and genotypic variation in Pleurotus species of Aotearoa, I first conducted a phylogenetic study to clarify the species boundaries within the genus (Chapter 2). I constructed a multi-gene phylogeny using ITS, LSU, RPB1, RPB2 and Tef markers. I discovered a cryptic indigenous subspecies within P. pulmonarius and resolved taxonomic ambiguities around P. djamor in Aotearoa. Confusion over species boundaries has previously led to the importation of this species, which has a potential for invasion and hybridisation with indigenous species. These refined species boundaries have significant implications for conservation and biosecurity.

Building on the refined species boundaries, I assessed how vegetative and reproductive growth traits vary between and within species. This study included three clonal replicates of 104 strains of five Pleurotus species grown in controlled conditions (Chapter 3). I discovered that intraspecific trait variation matched or exceeded interspecific variation, and found remarkably high levels of variation between clonal replicates of strains. Cultivated strains displayed less intraspecific variation than wild strains, suggesting the impact of cultivation history on phenotypic variation. My findings stress the necessity of true biological replication in mycology and challenge conventional definitions of individuality.

To understand genotypic variation within a wild-collected fungus, I conducted population genomic analyses and the first Pleurotus pangenome analysis using 29 P. purpureo-olivaceus strains from across the South Island (Chapter 4). I found a highly conserved core genome and overall genetic homogeneity, which was contrasted by diverse mating type loci and a large accessory genome. Instead of multiple populations isolated by distance or topographical barriers, my findings support a single panmictic South Island P. purpureo-olivaceus population with unrestricted gene flow.

Variation in fungi occurs at many levels and affects conservation, biodiversity, food production, and biotechnology. Both fundamental research and practical applications of fungi can benefit from considering the range of phenotypes and genotypes rather than species means and reference strains. My work contributes to a holistic understanding of fungal species and individuality, advancing fungal biology and informing cultivation practices and strategies for biodiversity conservation in the face of global environmental change. The diversity of Pleurotus phenotypes supports the identification of productive strains for indigenous oyster mushroom cultivation to enhance agricultural resilience, although further research and collaboration with indigenous communities – iwi Māori – are essential to ensure appropriate benefit sharing.