Abstract
Traditional population genetic methods are based on models that were developed for simple haploid mating systems. The assumptions behind these models are inconsistent with what is known about fungal biology. This modelling mismatch might affect the accuracy of population genetic inferences when studying fungi. I develop a model for the population genetics of Agaricomycete (mushroom-forming) fungi that is an extension of the Wright-Fisher model and explicitly captures the changes in ploidy through the Agaricomycete lifecycle. Changes in allele frequencies behave similarly to a slowed Wright-Fisher process, but the model can predict genotype frequencies differing from the standard Hardy-Weinberg equilibrium. This might mean excess homozygosity or excess heterozygosity, depending on the relative rates of mating between two monokaryons and mating between a dikaryon and a monokaryon, suggesting the model is useful and provides new inferences. Under coalescent process associated with the agaricomycete model, I calculate the expected time until two lineages coalescence. I then investigate the genetic structure of a real life fungal population using the charismatic fungus Amanita muscaria in populations around Dunedin, New Zealand. I construct a new high quality reference genome for A. muscaria and use resequencing of 96 individuals from five populations to investigate population parameters. This approach delivered a powerful dataset with 1,270,000 SNPs which were filtered to provide a working set of 313,000. Despite this power I identify surprisingly little population structure over distances of less than 10km, but do observe cases of clonality and likely inbreeding in some populations. Finally, I investigate the mating system of A. muscaria using the new agaricomycete model and genomic methods, which suggested a bipolar mating system with at least one functional mating locus, that appears to have at least three mating type alleles.