Evolutionary Genetics of Fungi Chapter Abstracts

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With the recent embrace of DNA sequencing techniques and phylogenetic methods by mycologists, fungal systematics is now in a state of transition. Traditionally, the fungi were classified with the plants. However, they have recently been shown to be more closely related to the animals and some protist groups and are now classified in their own Kingdom. The Kingdom Fungi includes the traditional Ascomycota, Basidiomycota, Zygomycota, and Chytridiomycota, while the Oomycota, the hyphochytrids, and the plasmodial and cellular slime molds, once considered to be fungi, are now classified in elsewhere in the eukaryotes. In contrast, several groups of organisms never previously classified in the fungi have been shown to be evolutionary related to the fungi, for instance, the animal pathogens Microsporidia and Pneumocystis. Molecular phylogenies indicate an early divergence of the chytrids. The Blastocladiales, traditionally classified in the Chytridiomycota, have closer evolutionary affinities with some groups of zyg

Chapter 2
Diversity and Biogeography of Higher Fungi in China
Zhu L. Yang

China is extraordinarily rich in higher fungi. Given that the number of fungi (including lichens) occurring in a given area is about 6 times that of vascular plants, about 180,000 fungal species may exist in China. Significant progresses have been made in field investigations and the studies of the Chinese mycobiota in the last thirty years. Nearly 8000 species belonging to about 1450 genera of higher fungi including lichens have been reported from China to date. About 40 volumes of the Flora Fungorum Sinicorum will become available soon. This review focuses on three prominent diversity regions of higher fungi in China: the eastern Himalayas and Hengduan Mts., central China, and the Chinese tropical regions. I summarize our currently understanding on how geological, geographical, historical, evolutionary, environmental, and ecological factors might have contributed to the patterns of diversity of the higher fungi in China.

Chapter 3
Biological Concepts of Vegetative Self and Nonself Recognition in Fungi
O. Cristina Micali and Myron L. Smith

The concepts of self and nonself have been a subject of much study and discussion in biology and philosophy. A significant volume of research on the subject has answered some but also generated many more questions. What defines self? What mechanisms control self and nonself recognition? What is the purpose of such a recognition system? A product of the post-World War II early immunology movement, the concept of self and non-self was introduced in clinical studies as a revolutionary metaphor for immune reactivity. In fungi, self and nonself recognition had been described almost one hundred years earlier as demarcation lines between genetically different mycelia growing on the same substrate. Since then, research has progressed to unravel the genetic basis for nonself recognition, the biochemical mechanisms involved in the incompatibility reactions and the evolutionary forces acting on these systems. This chapter is intended as a brief review of some of these scientific achievements.

Chapter 4
Fundamentals of Fungal Molecular Population Genetic Analyses
Jianping Xu

The last two decades have seen tremendous growth in the development and application of molecular methods in the analyses of fungal species and populations. In this chapter, I provide an overview of the molecular techniques and the basic analytical tools used to address various fundamental population and evolutionary genetic questions in fungi. With increasing availability and decreasing cost, DNA sequencing is becoming a mainstream data acquisition method in fungal evolutionary studies. However, other methods, especially those based on the polymerase chain reaction, remain powerful in addressing specific questions for certain groups of taxa and specific questions. These developments are bringing fungal population and evolutionary genetics into mainstream ecology and evolutionary biology.

Chapter 5
The Population Genetics of Phycomycetes
Timothy Y. James

The phycomycetes are an informal taxonomic group containing both true Fungi and heterotrophic protists (e.g., Oomycota). These fungi are microscopic, but ubiquitous, and reproduce mitotically through either zoospores (flagellated spores) or sporangiospores. This review covers the basic population genetics of the phycomycetes and highlights several well-studied species. Phycomycetes differ from the higher fungi (Ascomycetes and Basidiomycetes) in a number of ways that have profound impacts on their population genetics. Both diploidy and polyploidy are relatively common, if not the norm, whereas, a dikaryotic stage is absent altogether. A vegetative incompatibility response is also not observed in phycomycetes, and the size of the individual is believed to be spatially limited. Well studied examples of phycomycete pathogens, e.g., Phytophthora infestans, show evidence for a clonal epidemic population structure. This review includes the arbuscular mycorrhizal fungi (Glomeromycota) and discusses the ongoing d

Chapter 6
Population Genetics of Ascomycetes Pathogenic to Humans and Animals
Claude Pujol, Andrew Dodgson, and David R. Soll

Many pathogenic ascomycetes have no known sexual cycle and because they all can multiply by mitosis, have historically been considered to be clonal. This suggested, without expressly being stated, that strains were clones and, as a corollary, that genomes were stable in time, evolving linearly through mutations. During the last decade, this simplistic view has been altered for several of these species by the remarkable progress of molecular biology and genomics, and the use of population genetics analyses. While the former two methods can elucidate the molecular machinery involved in mating processes, including identification of opposite mating types and the mating event, the last method assesses the population structure of natural populations and their main mode of reproduction. Candida albicans, the most common pathogenic fungi, has been extensively studied. Through a critical review of the C. albicans literature, we will highlight the recent advances in our understanding of its parasexual cycle, population

Chapter 7
Molecular Population Genetics of Basidiomycete Fungi
Jianping Xu, Mingjie Cheng, Qi Tan, and Yingjie Pan

The last two decades have seen a dramatic increasing use of molecular tools in the analyses of basidiomycete populations. As a result, answers to many previously un-answerable but fundamental questions are beginning to emerge. In this chapter, we review the current literature and summarize our understandings of the population genetics of basidiomycete fungi. We pay specific attention to two model species, the edible button mushroom Agaricus bisporus and the human pathogenic yeast Cryptococcus neoformans. Other species we discussed include Armillaria gallica, Hebeloma cylindrosporum, Pleurotus spp.; Rhizoctonia solani, Heterobasidion annosum, Schizophyllum commune, and the Shiitake mushroom Lentinula edodes. These selected species of saprophytic, plant-associated and human-associated fungi were presented to illustrate the utilities of molecular markers in addressing questions related to: (i) the size and longevity of genets; (ii) the patterns of genetic variation within individual basidiomycete populations; (i

Chapter 8
Fungal Mitochondrial Inheritance and Evolution
Zhun Yan and Jianping Xu

Mitochondrion exists in virtually all eukaryotes. Because of its vital metabolic function, small genomes, and distinct patterns of inheritance, mitochondrial genes and genomes have attracted much attention in the last several decades. In this chapter, we review our current understandings of fungal mitochondrial genome structure and inheritance. Twenty-eight whole fungal mitochondrial genome sequences are available in the public databases. These genomes vary greatly in size, gene content and gene order. Interestingly, unlike the relatively uniform pattern of mitochondrial inheritance in plants and animals, fungal mitochondrial genomes exhibit diverse patterns of inheritance. In addition, both strain background and environmental conditions for mating can influence mitochondrial inheritance in fungi. We suggest that fungal mitochondrial genomes can serve as models for understanding the origin and evolution of mitochondria and the ubiquitous uniparental mitochondrial inheritance in plants and animals.

Chapter 9
Evolution of Drug Resistance in Pathogenic Fungi
Brian G. Oliver, Peter M. Silver, and Theodore C. White

Opportunistic fungal infections are increasing in incidence, in part due to an increase in the immunocompromised patient population. With an increased incidence comes an increase in resistance to antifungal drugs. This chapter details the development of drug resistance in pathogenic fungi, with an emphasis on Candida albicans. It details the genes involved in resistance, and the mechanisms that regulate those genes. The molecular mechanisms of resistance are placed in an evolutionary context, with an emphasis on the phylogeny of the organisms associated with resistance and the phenotypes that appear to be associated with the development of resistance.

Chapter 10
Rates and Effects of Spontaneous Mutations in Fungi
Clifford Zeyl

Despite the fact that spontaneous mutations are both the basis of much research and the raw material of evolution, major advances in our quantitative and qualitative understanding of mutation have come only recently. Mutation rates have been estimated for Aspergillus nidulans, Cryptococcus neoformans, Neurospora crassa and Saccharomyces cerevisiae, and are consistently below 0.008. Distributions of fitness costs of these mutations appear to include substantial fractions of mutations with large effects, but laboratory fitness estimates are generally insensitive to effects less than 1% and these are the mutations most critical to the long-term health of small populations. The dominance and epistasis of spontaneous mutations are also important attributes, potentially playing major roles in the evolution of sex and ploidy. Mutation can alter the life cycle by inactivating functions required for sex, particularly when sex is already facultative. Adaptive mutations in yeast occur at rates on the order of 10^-11, and

Chapter 11
Cryptococcus neoformans Evolves as a Model of Choice for Studying Signal Transduction
Ping Wang and Deborah S. Fox

Among pathogenic fungi, Cryptococcus neoformans has begun to gain popularity as an experimental model organism for the study of pathogenesis. This is largely due to its clinical significance, defined and genetically tractable life cycle, sequenced genome, and the contributions of many dedicated investigators. Research subjects have been diverse, ranging from morphogenesis, population and evolution biology, biochemistry, molecular genetics, and pathobiology. With the introduction of genomic and proteomic technology and other modern approaches into the field, it is expected that this trend will continue at an unprecedented pace. Here we provide a brief review on how C. neoformans evolved to be a model for studying the roles of signal transduction in fungal pathogenesis.

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