UC Berkeley

The genus of Ascomycete molds, Neurospora, has served as a valuable model for the cellular and molecular biology of multicellular fungi, and more recently for the evolution of fungi. In this thesis I present three studies of Neurospora which each expand the knowledge and utility of this model.

First, I expand collections of rare Neurospora species by 113 strains and 149 whole genome sequences, including the first conidial homothallic (self-fertile) Neurospora as well as genome sequences for endolichenic Neurospora from two species, both aconidial. These data provide insight into Neurospora’s mysterious lifestyle, and show that at least some Neurospora species live part of their lives as endosymbionts. These collections also expand the utility of Neurospora as a model for breeding system evolution by showing that every combination of reproductive system seen in Ascomycota is also seen in Neurospora.

Second, I use this collection of genomes, along with 43 previously published genomes, to study the population biology of Neurospora species with diverse reproductive ecologies. While homothallic Neurospora had previously been assumed to be dominantly or exclusively selfing, I show that at least one aconidial homothallic lineage is recombining at least as much as heterothallic (self-sterile) species. I further detail the population structure and biogeography of diverse groups of Neurospora, showing how differing ecologies and mating paradigms work at different scales to shape populations.

Third, I address the question: How does the rate of genomic rearrangements vary across the genome? Genomic rearrangements are an important source of adaptive variation, but studying them has been challenging due to a lack of suitable (i.e. whole genome) data

and the computational complexity of the problem. Leveraging this collection of Neurospora genomes, I present a method to estimate the rearrangement rate across the genome. I phrase the problem in graph theoretic terms and find it to be an instance of the well known clique cover problem. I use this method to find evidence that in N. crassa, like other Eukaryotes, rearrangements are more common in the subtelomeric regions of the chromosomes, which facilitates the evolution of novel genes.