Note: The Mycota -- Editor's page -- Copyright -- Series Preface -- Addendum to the Series Preface -- Volume Preface -- Contents Part B -- Contents Part A -- List of Contributors -- The Fungal Hierarchy -- 1 Basidiomycetous Yeasts -- 2 Urediniomycetes -- 3 Ustilaginomycetes1 -- 4 Heterobasidiomycetes -- 5 Basidiomycota: Homobasidiomycetes -- Nomenclature and Documentation -- 6 The Naming of Fungi -- 7 Cultivation and Preservation of Fungi in Culture -- 8 Computer-Assisted Taxonomy and Documentation -- Evolution and Speciation -- 9 Speciation Phenomena -- 10 Fungal Molecular Evolution: Gene Trees and Geologic Time -- Subject Index -- Biosystematic Index.

Note: Intro -- Series Preface -- Volume Preface to the Second Edition -- Volume Preface to the First Edition -- Contents -- List of Contributors -- 1 Fungi from PCR to Genomics: The Spreading Revolution in Evolutionary Biology -- I. PCR to Genome Sequencing and a Robust Phylogeny for Fungi -- II. Peering into Variation Among Individuals: Next-Generation Sequencing -- III. Fungal Species Recognition in Era of Population Genomics -- IV. Metagenomics and Tools for Identification -- V. What Is a Fungus? Phenotype and Its Evolutionary Origins -- A. Discoveries of Protistan Allies Affect Definitions of Fungi and Animals -- B. Evolutionary Origin of Characters That Define Fungi -- 1. Fungus-Specific Chitin Synthases -- 2. Biosynthesis of Ergosterol, the Characteristic Sterol in Fungal Membranes -- 3. Origins of Fungal Lysine Biosynthetic Pathway in Opisthokont Prehistory -- 4. Hyphae and Absorptive Nutrition Were Missing from Fungal Stem Lineage -- V. Convergent Evolution of Funguslike Protists -- VII. Conclusion -- References -- Fungal-Like Organisms -- 2 Excavata: Acrasiomycota -- Amoebozoa: Dictyosteliomycota, Myxomycota -- I. Introduction -- II. Acrasiomycota -- III. Dictyosteliomycota -- A. Life Cycle -- B. Distribution and Occurrence -- C. Isolation -- D. Taxonomy -- IV. Myxomycota -- A. Life Cycle -- B. Taxonomy -- C. Distribution and Occurrence -- V. Ecological Significance -- References -- 3 Systematics of the Straminipila: Labyrinthulomycota, Hyphochytriomycota, and Oomycota -- I. Introduction -- II. Molecular Phylogeny and Systematics -- A. Higher-Level Relationships -- B. Systematics of Labyrinthulomycota -- C. Systematics of Hyphochytriomycota -- D. Systematics of Oomycota -- E. Early Diverging Clades: Classes Incertae Sedis -- 1. Eurychasmales -- 2. Haptoglossales -- 3. Olpidiopsidales s. lat. -- 4. Haliphthorales -- F. Saprolegniomycetes. , 1. Atkinsiellales -- 2. Leptomitales s. lat. and Related Clades -- 3. Saprolegniales -- a) Verrucalvaceae -- b) Achlyaceae -- c) Saprolegniaceae -- G. Peronosporomycetes -- 1. Rhipidiales -- 2. Albuginales -- 3. Peronosporales s. lat. -- a) Salisapilaceae -- b) Pythiaceae s. lat. -- c) Peronosporaceae s. lat. -- (iv) Part 1: Phytopythium and Halophytophthora Clades -- (v) Part 2: Phytophthora Clades -- (vi) Part 3: Downy Mildew Clades -- III. Selected Developmental and Morphological Trends -- A. Zoospore Characteristics -- 1. Zoospore Morphology and Flagellar Rootlet Organization -- 2. Encystment/Adhesive Vesicles -- B. Life Histories and Sexual Cycle Characteristics -- IV. Evolutionary Timeline and the Fossil Record -- V. Conclusions -- References -- 4 Rhizaria: Phytomyxea -- I. Introduction -- II. Life Cycle -- A. Sporogenic (Secondary) Plasmodia -- B. Sporangial (Primary) Plasmodia -- C. Relationship of Life Cycle Phases -- D. Karyogamy -- III. Classification -- A. Phylogeny -- B. Genera and Species -- C. Molecular Applications -- IV. Occurrence, Distribution, Maintenance, and Culture -- V. Conclusions and Future Prospects -- References -- Fungi -- 5 Microsporidia -- I. Introduction -- II. Occurrence and Distribution -- A. Arthropod Hosts -- B. Aquatic Hosts (Marine and Freshwater) -- C. Mammalian and Avian Hosts -- III. Morphology of the Microsporidian Spore -- A. General Description and Common Features -- B. Species (Spores) Infecting Arthropod Hosts -- C. Species (Spores) Infecting Aquatic Hosts -- D. Species (Spores) Infecting Mammalian and Avian Hosts -- IV. Microsporidian Invasion Apparatus -- V. Life Cycle -- A. Species Infecting Arthropod Hosts -- B. Species Infecting Aquatic Hosts -- C. Species Infecting Mammalian and Avian Hosts -- VI. Systematics and Evolution -- VII. Classification -- VIII. Maintenance and Culture. , A. Species Infecting Arthropod Hosts -- B. Species Infecting Aquatic Hosts -- C. Species Infecting Mammalian and Avian Hosts -- IX. Conclusions -- References -- 6 Chytridiomycota, Monoblepharidomycota, and Neocallimastigomycota -- I. Introduction -- II. Occurrence and Dispersal -- III. Culture and Maintenance -- IV. Phylogenetic Concepts of Zoosporic Fungi -- V. Identification of Zoospore Ultrastructural Characters and Character States -- VI. Characterization of Phyla -- A. Chytridiomycota -- 1. Rhizophydiales -- 2. Chytridiales -- 3. Cladochytriales -- 4. Lobulomycetales -- 5. Polychytriales -- 6. Spizellomycetales -- 7. Rhizophlyctidales -- 8. Synchytrium Lineage -- 9. Blyttiomyces helicus Lineage -- B. Monoblepharidomycota -- C. Neocallimastigomycota -- VII. Evolution -- VIII. Conclusions -- References -- 7 Blastocladiomycota -- I. Introduction -- II. Occurrence and Distribution -- A. Saprobic Species -- B. Invertebrate Parasitic Species -- C. Plant-Pathogenic Species -- D. Mycoparasites -- E. DNA-Based Evidence -- III. Structure of Thallus and Reproductive Characters -- IV. Phylogeny and Systematics -- A. Phylogenetic Placement of Blastocladiomycota -- B. Phylogenetic Classification of Blastocladiomycota -- V. Life Cycles -- A. Historical Perspective -- B. Life Cycles of Allomyces -- C. Life Cycles of Other Blastocladiomycota -- VI. Zoospore Ultrastructure -- A. Historical Perspective -- B. Generalized Structure of Motile Cells of Blastocladiomycota -- 1. Axial Assembly -- 2. Microbody-Lipid Globule Complex -- 3. Flagellar Apparatus -- 4. Cytoplasmic Inclusions -- VII. Genetics and Physiology -- A. Hybridization -- B. Mitosis -- C. Taxis -- D. Substrate Utilization and Respiration -- E. Genomics -- VIII. Conclusions and Future Directions -- References. , 8 Zygomycetous Fungi: Phylum Entomophthoromycota and Subphyla Kickxellomycotina, Mortierellomycotina, Mucoromycotina, and Zoop... -- I. Introduction -- II. Occurrence and Distribution -- III. Economic Importance and Biology -- A. Food -- B. Plant Pathogens (Choanephora Fruit Rot) and Storage Rots -- C. Zygomycosis -- D. Industrial Uses of Zygomycotan Fungi: Biotechnology, Biodegradation, Biosorption, Bioremediation, Biotransformation -- E. Mucorales and Endobacteria -- F. Light -- G. Mating -- IV. Development of Taxonomic Theory -- V. Reproduction and Dispersal -- A. Growth -- B. Dispersal -- VI. Classification -- A. Phylum, Subphyla, Classes, and Orders -- B. Ordinal Distribution -- C. Phylum Entomophthoromycota (Fig.8.1) -- 1. Morphology -- a) Vegetative Structures -- b) Asexual Spores (Conidia) -- c) Auxiliary Hyphal Structures -- d) Resting Spores -- 2. Taxonomy to Classes and Orders -- a) Basidiobolomycetes and Basidiobolales -- b) Entomophthoromycetes and Entomophthorales s.s. -- i. Entomophthorales Sensu Humber (2012a) and Four Families (Ancylistaceae, Completoriaceae, Entomophthoraceae, Meristacraceae) -- c) Neozygitomycetes and Neozygitales -- D. Nonentomophthoralean Subphyla (Kickxellomycotina, Mortierellomycotina, Mucoromycotina, Zoopagomycotina) -- 1. Mitospores -- a) Sporangiospores -- b) ``Conidia´´ Versus True Conidia -- 2. Endospore-Forming Structures -- a) Sporangia -- b) Sporangiola -- c) Merosporangia -- 3. Thallospores -- a) Arthrospores -- b) Chlamydospores -- c) Yeast Cells -- 4. Meiospores -- a) Zygospores -- b) Azygospores -- 5. Kickxellomycotina -- a) Asellariales -- b) Dimargaritales -- c) Harpellales -- d) Kickxellales -- 6. Mortierellomycotina and Mortierellales -- 7. Mucoromycotina -- a) Endogonales -- b) Mucorales -- 8. Zoopagomycotina and Zoopagales -- VII. Maintenance and Culture -- VIII. Conclusions -- References. , 9 Glomeromycota -- I. Introduction -- II. Arbuscular Mycorrhizal Symbiosis -- III. Morphology and Reproduction -- IV. Dispersal and Host Relations -- A. Geographical Distribution -- B. Host Specificity -- V. Development of Taxonomic Theory -- VI. Classification -- A. Phylum Characteristics -- B. Morphological Criteria Used for Classification -- C. Orders and Families (For an Overview See Table9.1) -- 1. Glomerales J.B. Morton and Benny (Sensu Schüßler et al. 2001b) -- a) Glomeraceae Piroz. and Dalpé -- b) Claroideoglomeraceae C. Walker and A. Schüßler -- 2. Diversisporales C. Walker and A. Schüßler -- a) Gigasporaceae J.B. Morton and Benny -- b) Acaulosporaceae J.B. Morton and Benny -- c) Pacisporaceae C. Walker, Blask., A. Schüßler and Schwarzott -- (d) Diversisporaceae C. Walker and A. Schüßler -- 3. Paraglomerales C. Walker and A. Schüßler -- a) Paraglomeraceae J.B. Morton and D. Redecker -- 4. Archaeosporales C. Walker and A. Schüßler -- a) Archaeosporaceae J.B. Morton and D. Redecker -- b) Ambisporaceae C. Walker, Vestberg and A. Schüßler -- c) Geosiphonaceae Engler and Gilg, Emend. A. Schüßler -- 5. Familia Incertae Sedis -- a) Entrophosporaceae Oehl and Sieverd -- D. Species Concepts -- VII. Evolution of the Phylum -- A. Ecological Aspects -- B. Spore Structure and Ontogeny -- C. Evidence from Fossil Record and Patterns of Association with Plants -- IX. Conclusion -- References -- 10 Pucciniomycotina -- I. Introduction -- II. Systematics of Pucciniomycotina -- III. Diversity -- A. Ecological Diversity -- B. Life Cycles -- C. Morphological and Genomic Diversity -- D. Species Discovery and Diversity -- IV. Classification -- A. Agaricostilbomycetes -- B. Atractiellomycetes -- C. Classiculomycetes -- D. Cryptomycocolacomycetes -- E. Cystobasidiomycetes -- F. Microbotryomycetes -- G. Mixiomycetes -- H. Pucciniomycetes -- I. Tritirachiomycetes. , V. Culturing.

Note: Intro -- Series Preface -- Volume Preface to the Second Edition -- Volume Preface to the First Edition -- Contents -- List of Contributors -- Fungi -- 1 Saccharomycotina and Taphrinomycotina: The Yeasts and Yeastlike Fungi of the Ascomycota -- I. Introduction -- II. Occurrence, Distribution, and Ecology -- III. Importance -- A. Food, Beverage, and Industrial Uses -- B. Agriculturally Important Yeasts -- 1. Plant Pathogens -- 2. Biocontrol Yeasts -- C. Food and Beverage Spoilage -- D. Human and Animal Pathogens -- IV. Reproduction -- A. Asexual -- 1. Budding, Fission, Endospores, Chlamydospores -- 2. Pseudohyphae and True (Septate) Hyphae -- B. Sexual Reproduction -- V. Taxonomic Methods -- A. Phenotypic Characterization -- B. Genotypic Characterization -- VI. Phylogeny and Classification -- A. Phylogeny -- B. Classification -- 1. Saccharomycotina -- 2. Taphrinomycotina -- VII. Isolation, Maintenance, and Culture Availability -- A. Isolation -- B. Maintenance -- C. Culture Availability and Distribution -- VIII. Future Directions -- References -- 2 Pezizomycotina: Pezizomycetes, Orbiliomycetes -- I. Introduction -- II. Orbiliomycetes: An Overview -- III. Occurrence and Distribution -- A. Species Trapping Nematodes and Other Invertebrates -- B. Saprobic Species -- IV. Morphological Features -- A. Ascomata -- B. Asci -- C. Ascospores -- D. Paraphyses -- E. Septal Structures -- F. Nuclear Division -- G. Anamorphic States -- V. Reproduction -- VI. History of Classification and Current Hypotheses -- VII. Growth in Culture -- VIII. Pezizomycetes: An Overview -- IX. Occurrence and Distribution -- A. Parasitic Species -- B. Mycorrhizal Species -- C. Saprobic Species -- X. Morphological Features -- A. Ascomata -- B. Asci -- C. Ascospores -- D. Paraphyses -- E. Septal Structures -- F. Anamorphic States -- XI. Reproduction. , XII. History of Classification and Current Hypotheses -- A. Families of the Pezizomycetes -- 1. Ascobolaceae -- 2. Ascodesmidiaceae -- 3. Caloscyphaceae -- 4. Chorioactidaceae -- 5. Discinaceae -- 6. Glaziellaceae -- 7. Helvellaceae -- 8. Karstenellaceae -- 9. Morchellaceae -- 10. Pezizaceae -- 11. Pyronemataceae -- 12. Rhizinaceae -- 13. Sarcoscyphaceae -- 14. Sarcosomataceae -- 15. Tuberaceae -- XIII. Growth in Culture -- XIV. Conclusion -- References -- 3 Pezizomycotina: Sordariomycetes and Leotiomycetes -- I. Introduction -- II. Sordariomycetes -- A. Ecology -- B. Morphology -- 1. Ascomata -- 2. Centrum Development -- 3. Asci -- 4. Ascospores -- 5. Anamorphs -- 6. Ultrastructure -- C. Molecular Phylogeny -- D. Classification -- 1. Hypocreomycetidae -- a) Coronophorales -- b) Glomerellales -- c) Hypocreales -- d) Melanosporales -- e) Microascales -- 2. Sordariomycetidae -- a) Calosphaeriales -- b) Diaporthales -- c) Magnaporthales -- d) Ophiostomatales -- e) Boliniales -- f) Chaetosphaeriales -- g) Coniochaetales -- h) Sordariales -- 3. Xylariomycetidae -- 4. Orders Incertae Sedis -- a) Koralionastelales -- b) Lulworthiales -- c) Meliolales -- d) Phyllachorales -- e) Trichosphaeriales -- III. Leotiomycetes -- A. Classification History -- 1. History of Leotiomycetes -- 2. Current Classification of Leotiomycetes -- B. Molecular Phylogeny Update -- 1. Higher-Level Relationships of Leotiomycetes -- 2. Phylogeny Within Leotiomycetes -- C. Characters -- 1. Apothecium (Ascoma) Morphology, Anatomy, and Ultrastructure -- 2. Ecology and Biogeography -- IV. Geoglossomycetes -- V. Laboulbeniomycetes -- A. Laboulbeniales -- B. Pyxidiophorales -- VI. Problems and Perspectives -- A. Genome Project -- B. Environmental Study -- VII. Culture and Maintenance -- VIII. Conclusion -- References -- 4 Pezizomycotina: Lecanoromycetes -- I. Introduction. , II. Occurrence and Distribution -- III. Substrate Range and Ecology -- A. Substrate Range -- B. Lifestyles -- C. Mycobiont-Photobiont Associations -- IV. Mycobiont-Photobiont Cellular Contacts -- V. Morphological and Chemical Features -- A. Thalli -- B. Ascomata -- 1. Ascoma Morphology -- 2. Ascoma Development -- C. Asci -- 1. Ascus Walls -- 2. Ascus Apical Structure -- 3. Dehiscence Mechanisms -- D. Ascospores -- E. Interascal Filaments -- F. Pycnidia -- G. Asexual Propagules -- H. Secondary Compounds -- VI. Origin and Diversification -- VII. Orders and Classification -- A. Acarosporales -- B. Baeomycetales -- C. Caliciales -- D. Candelariales -- E. Lecanorales -- F. Lecideales -- G. Ostropales -- H. Peltigerales -- I. Pertusariales -- J. Rhizocarpales -- K. Sarrameanales -- L. Teloschistales -- M. Trapeliales -- N. Umbilicariales -- VIII. Conclusion -- References -- 5 Pezizomycotina: Eurotiomycetes -- I. Phylogeny and Taxonomy -- A. Eurotiomycetidae -- 1. Eurotiales -- a) Aspergillaceae -- i. Taxonomy -- ii. Asexual Morphology -- iii. Sexual Morphology and Self-Fertility -- b) Thermoascaceae -- i. Taxonomy -- ii. Asexual and Sexual Morphology -- c) Trichocomaceae -- i. Taxonomy -- ii. Asexual and Sexual Morphology -- d) Disputed Families: Monascaceae and Elaphomycetaceae -- 2. Onygenales -- a) Core Families of Onygenales -- b) Ajellomycetaceae -- 3. Arachnomycetales, Ascosphaera, and Eremascus -- 4. Coryneliales -- B. Chaetothyriomycetidae -- 1. Chaetothyriales -- 2. Verrucariales -- 3. Pyrenulales -- 4. Celotheliales ad int. (Gueidan et al. 2014) -- C. Taxa of Uncertain Placement -- 1. Mycocaliciomycetidae/Mycocaliciales -- 2. Marine Species of Dactylospora and Sclerococcum -- 3. Cirrosporium novae-zelandiae -- II. Ecology and Economic Importance -- A. Extremophilism -- B. Animal Pathogens -- 1. Onygenalean Pathogens. , a) Histoplasmosis, Blastomycosis, and Paracoccidioidomycosis -- b) Coccidioidomycosis or ``Valley Fever´´ -- c) Dermatophytes -- d) Chalkbrood of Bees -- 2. Eurotialean Pathogens -- C. Plant Pathogens -- D. Mutualistic Interactions -- 1. Ectomycorrhizae -- 2. Lichens -- 3. Myrmecophytes -- E. Food Contamination -- F. Food Production -- G. Toxic Secondary Metabolites -- H. Industrial Uses -- III. Summary -- References -- 6 Pezizomycotina: Dothideomycetes and Arthoniomycetes -- I. Introduction -- II. Character Evolution: Divergence and Convergence -- A. Morphology and Development -- B. Brief Taxonomic History -- III. Ecology and Distribution -- A. Associations with Plants and Plant Debris -- B. Aquatic Species -- C. Associations with Algae and Other Lichens -- D. Rock Environments and Oligotrophism -- IV. Modern Classification and Phylogeny -- A. Dothideomycetes -- 1. Pleosporomycetidae -- 2. Dothideomycetidae -- 3. Incertae Sedis Lineages -- B. Arthoniomycetes -- V. Maintenance and Culture -- VI. Conclusions -- References -- Nomenclature and Documentation -- 7 The Shifting Sands of Fungal Naming Under the ICN and the One Name Era for Fungi -- I. Introduction -- II. International Code of Nomenclature for Algae, Fungi, and Plants (ICN) -- A. Transition to One Name Per Fungus -- 1. History and Enactment of Rule Changes -- 2. How One Name Per Fungus Will Happen Under the New Rules -- B. Other Major and Minor Changes in the ICN -- 1. Effective Publication via Electronic Publication -- 2. Latin or English for Valid Publication of Names of New Taxa -- 3. Registration of Fungal Names -- 4. Minor Changes -- C. Practical Notes on Using the ICN -- 1. How Do I Describe New Taxa at the Rank of Species? -- a) Validation -- b) Legitimization -- 2. How Do I Describe New Taxa at the Rank of Genus? -- 3. What Is an Ex-type?. , 4. How and When Do I Designate a Lectotype for a Species? -- 5. How and When Do I Designate a Neotype for a Species? -- 6. How and When Do I Designate an Epitype for a Species? -- 7. How Do I Validly Publish New Combinations? -- 8. How Do I Validly Publish a Replacement Name Also Known as a Nomen Novum? -- 9. How Do I Correctly Give Author Citations for Taxa? -- III. Potential Changes to Nomenclatural Rules -- IV. Conspectus and the Future of Fungal Naming -- References -- 8 The Role of Herbaria and Culture Collections -- I. Introduction -- II. Best Practices for Fungal Herbaria -- A. Preparing Fungal Reference Specimens -- B. Preparing Dried Culture Specimens -- C. Numbering and Labeling Fungal Specimens -- D. Storage and Organization of Dried Specimens -- E. Requesting, Annotating, and Returning Specimens -- F. Use of Fungal Herbarium Specimens in Molecular Studies -- 1. Introduction -- 2. Contamination of Herbarium DNA Samples -- 3. Extraction of DNA from Herbarium Specimens -- 4. DNA Quality from Herbarium Specimens -- III. Maintenance of Living Cultures -- A. Introduction -- B. Metabolically Active Preservation -- 1. Storage on Agar with Periodic Transfer -- 2. Storage on Agar Under Mineral Oil and Distilled Water -- C. Metabolically Inactive Preservation -- 1. Cryopreservation (Cryogenic Storage) -- 2. Freeze Drying -- IV. Conclusions -- References -- Evolution -- 9 Subcellular Structure and Biochemical Characters in Fungal Phylogeny -- I. Introduction -- II. The Role of Subcellular Structure in Fungal Phylogeny -- III. The Role of Biochemical Characters in Fungal Phylogeny -- IV. Character and Character State Definition and Refinement -- V. Structural and Biochemical Database -- VI. Structural and Biochemical Database in Phylogenetic Analysis -- VII. Development of the Fungal Subcellular Ontology. , VIII. Specimen Preparation and Evaluation for Subcellular Structure.

Note: The Mycota -- Editor's page -- Copyright -- Series Preface -- Volume Preface -- Addendum to the Series Preface -- Volume Preface -- Contents Part A -- Contents Part B -- List of Contributors -- The Fungal Hierarchy -- 1 What are Fungi? -- 2 The Peronosporomycetes -- 3 Hyphochytriomycota -- 4 Plasmodiophoromycota -- 5 Chytridiomycota -- 6 Zygomycota: Zygomycetes -- 7 Zygomycota: Trichomycetes -- 8 Ascomycota -- 9 Ascomycetous Yeasts aud Yeastlike Taxa -- 10 The Monophyletic Plectomycetes: Ascosphaerales, Onygenales. Eurotiales -- 11 Pyrenomycetes - Fungi with Perithecia 1 -- 12 Discomycetes -- 13 Loculoascomycetes -- 14 The Taxonomy of Anamorphic Fungi -- Subject Index -- Biosystematic Index.

Note: Includes bibliographies and indexes