Sex, Alternative Lifestyles, and a Graphic Study of a Model

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) dataand 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

Sex, Alternative Lifestyles, and a Graphic Study of a Model

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) dataand 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

SNPs for full set of non-redundant sequences

This file contains SNPs for the 41 isolates of taxa PS4A, PS4B and PS6. Initially the dataset was comprised of 52 isolates, but after genome sequencing a "clone correction" was carried out, i.e. only one representative of groups of genome with genetic distance below 0.1 were kept in the dataset. The file used for clone correction has also been deposited on Dryad

SNPs used to identify redundant sequences

This files contains the SNPs that were used to identify redundant sequences. It is based on the file containing "SNPs for non-redundant European and North-American sequences", with missing data removed. It was analysed using DNADIST&NEIGHBOR programs in the PHYLIP Package, and a single representative of each clonal complex was kept in the dataset "SNPs for non-redundant European and North-American sequences" (clonal complex identified as groups of individuals with genetic distance <0.1

SNPs for non-redundant European and North-American sequences

This file contains SNPs for the European and North American isolates of PS4B. SNP-calling was performed independently for this set of sequences, for the full set of sequences and for the full set of non redundant sequences

Reply to Engelthaler and Meyer, "Furthering the Continental Drift Speciation Hypothesis in the Pathogenic Cryptococcus Species Complexes".

We thank and compliment Engelthaler and Meyer for their letter (1), which provides new information extending our hypothesis that continental drift was a major influence in driving speciation within the Cryptococcus species complexes (2). Their map superimposing the four major current Cryptococcus gattii molecular types/ species (VGI, VGII, VGIII, and VGIV) on the map of Pangea sheds light on possible origins of Asian, Indian, and Iberian isolates and clearly delineates areas that are unexplored and in need of sampling. We are encouraged by the notion that viewing cryptococcal speciation in the larger context of continental drift is already stimulating new thought, and we hope that it also catalyzes new experimental work to separate ancient speciation events in deep geologic time from more recent introductions of isolates in defined geographic areas

Reply to Engelthaler and Meyer, "Furthering the Continental Drift Speciation Hypothesis in the Pathogenic Cryptococcus Species Complexes".

We thank and compliment Engelthaler and Meyer for their letter (1), which provides new information extending our hypothesis that continental drift was a major influence in driving speciation within the Cryptococcus species complexes (2). Their map superimposing the four major current Cryptococcus gattii molecular types/ species (VGI, VGII, VGIII, and VGIV) on the map of Pangea sheds light on possible origins of Asian, Indian, and Iberian isolates and clearly delineates areas that are unexplored and in need of sampling. We are encouraged by the notion that viewing cryptococcal speciation in the larger context of continental drift is already stimulating new thought, and we hope that it also catalyzes new experimental work to separate ancient speciation events in deep geologic time from more recent introductions of isolates in defined geographic areas

Continental Drift and Speciation of the Cryptococcus neoformans and Cryptococcus gattii Species Complexes.

Genomic analysis has placed the origins of two human-pathogenic fungi, the Cryptococcus gattii species complex and the Cryptococcus neoformans species complex, in South America and Africa, respectively. Molecular clock calculations suggest that the two species separated ~80 to 100 million years ago. This time closely approximates the breakup of the supercontinent Pangea, which gave rise to South America and Africa. On the basis of the geographic distribution of these two species complexes and the coincidence of the evolutionary divergence and Pangea breakup times, we propose that a spatial separation caused by continental drift resulted in the emergence of the C. gattii and C. neoformans species complexes from a Pangean ancestor. We note that, despite the spatial and temporal separation that occurred approximately 100 million years ago, these two species complexes are morphologically similar, share virulence factors, and cause very similar diseases. Continuation of these phenotypic characteristics despite ancient separation suggests the maintenance of similar selection pressures throughout geologic ages

Population genomics of Neurospora Insights Into the Life History of a Model Microbial Eukaryote

International audienceThe ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research

Clonal reproduction in fungi

Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305–E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest