Fungal populations and species /

Fungal populations and species /

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Bibliographic Details
Author / Creator:Burnett, J. H. (John Harrison), 1922-2007
Imprint:Oxford ; New York : Oxford University Press, 2003.
Description:xiii, 348 p. : ill., maps ; 25 cm.
Language:English
Subject:
Fungi -- Genetics.
Fungi -- Speciation.
Fungi -- Genetics.
Format: Print Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/4872835
Hidden Bibliographic Details
ISBN:0198515529
0198515537 (pbk.)
Notes:Includes bibliographical references and index.
Table of Contents:
  • Introduction
  • Part I. Basic mycology
  • 1. Elements of classification, structure, sexuality, biology and genetics of Fungi
  • 1.1. Elements of classification
  • 1.1.1. Convention on the use of names in mycology
  • 1.2. Life cycles
  • 1.3. Structural considerations
  • 1.3.1. Hyphae and mycelia
  • 1.3.2. Dimorphism
  • 1.3.3. Perennating structures
  • 1.3.4.. Spores and conidia
  • 1.4. Sexual reproduction and sexuality
  • 1.4.1. Mating systems
  • 1.5. Dispersal
  • 1.6. Aspects of fungal biology of genetic significance
  • 1.6.1. Clones
  • 1.6.2. Phenotypic plasticity
  • 1.6.3. Pleomorphism
  • 1.6.4. Heterokaryosis and the parasexual cycle
  • 1.6.5. Chromosomal DNA and cytology
  • 1.6.6. Cytoplasmic organelles and other inherited cytoplasmic components
  • 1.7. A simplified classification of the fungi
  • Further reading
  • Part II. Methodology
  • 2. Genetic markers for population studies--I Morphological, physiological and cytological markers
  • 2.1. Morphological markers
  • 2.2. Mating-type factors
  • 2.3. Somatic incompatibility (SI)
  • 2.3.1. SI in Ascomycotina and Fungi Anamorphici
  • 2.3.1.1.. Recognizing SI in Ascomycotina
  • 2.3.1.2.. Heterokaryon self-incompatibility
  • 2.3.1.3.. SI in similar or related taxa
  • 2.3.1.4.. SI genetics
  • 2.3.1.5.. Complex SI behaviour
  • 2.3.2. SI in Basidiomycotina
  • 2.3.2.1. Recognizing SI in Basidiomycotina
  • 2.3.2.2. Complex SI
  • 2.3.2.3. Monokaryotic homogenic incompatibility in Basidiomycotina
  • 2.3.2.4. Spatial extent of SI genets
  • 2.3.2.5. SI genetics
  • 2.4. Pathogenic markers
  • 2.4.1. Virulence characters
  • 2.4.1.1. Virulence genetics
  • 2.4.2. Aggressiveness
  • 2.5. Fungicide resistance as a marker
  • 2.6. Cytological markers
  • 2.6.1. Chromosomal techniques
  • 2.6.2. Electrophoretic chromosomal techniques
  • 2.6.3. Karyotyping procedures
  • Further reading
  • 3. Genetic markers for population studies--II Molecular markers
  • 3.1. Specific molecules
  • 3.2. Proteins and polymorphic enzymes
  • 3.3. Nucleic acids
  • 3.3.1. The use of whole DNA molecules
  • 3.3.2. The polymerase chain reaction
  • 3.3.2.1. Primers for PCR
  • 3.3.3. Random amplified polymorphic DNA (RAPD)
  • 3.3.3.1. Template-mixed RAPDs
  • 3.3.3.2. Sequence-characterized amplified regions (SCARs)
  • 3.3.3.3. RAPD with single-strand conformational polymorphism (RAPD-SSCP or SSCP)
  • 3.3.3.4. Denaturing gradient gel electrophoresis (DGGE or CDGE)
  • 3.3.3.5. Variable numbers of tandem repeats (VNTRs)
  • 3.3.3.6. Simple sequence repeats or microsatellites (SSRs)
  • 3.3.3.7. Random amplified microsatellites (RAMs)
  • 3.3.4. Amplified fragment-length polymorphism (AFLPs)
  • 3.3.5. The analysis of nucleotide fragments
  • 3.3.5.1. Sequencing
  • 3.3.5.2. Restriction fragment length polymorphisms (RFLPs)
  • 3.3.5.3. The use of probes with RFLPs: Southern blots
  • 3.3.5.4. Amplified fragments
  • 3.4. The utility of different molecular screening techniques
  • 3.5. Taxonomic identification using sequence markers
  • Further reading
  • 4. Defining fungal individuals: ecological, biological and genetical aspects; sampling
  • 4.1. The physical and biological attributes of fungal genets
  • 4.1.1. Mycelial extent
  • 4.1.2. Substrate specificity and specific site locations
  • 4.1.3. Persistence
  • 4.1.4. Propagule dispersal and cloning
  • 4.2. Recognition of intraspecific groups, genets and fungal individuals
  • 4.2.1. Using the SI reaction
  • 4.2.2. Using pathogenicity characters
  • 4.2.3. Using molecular markers
  • 4.2.4. Summation
  • 4.3. Sampling
  • 4.3.1. Spatial sampling procedures
  • 4.3.1.1. Site sampling
  • 4.3.1.2. Sample size
  • 4.3.1.3. Pattern recognition
  • 4.3.1.4. Practical techniques for isolating and recognizing fungi
  • Further reading
  • 5. Describing and analysing populations: basic genetic and phylogenetic aspects
  • 5.1. Phenotypic and genetic diversity
  • 5.1.1. Phenotypic diversity
  • 5.1.2. Phenotypic similarity and dissimilarity
  • 5.1.2.1. Similarity
  • 5.1.2.2. Dissimilarity
  • 5.1.3. Genetic and genotypic diversity
  • 5.1.4. Comparing genetic variation within subdivided populations or between populations
  • 5.2.. Character association: the recognition of distinct genotypic groups and their relationships
  • 5.2.1. ANOVA and AMOVA
  • 5.2.2. Ordination methods
  • 5.2.3. Hierarchical methods
  • 5.2.3.1. Distance methods
  • 5.2.3.2. Discrete character methods
  • 5.2.3.3. Estimating the likelihood of any tree and discriminating between alternative trees
  • 5.3.. Population history: the coalescent and nested clade analysis
  • Further reading
  • Part III. Processes in populations
  • 6. The generation of variation--I Mutation and migration
  • 6.1. The establishment of mutants, random genetic change and the frequency of detectable mutations
  • 6.1.1. Genetic hitch-hiking
  • 6.1.2. The frequency of mutation in fungal chromosomes
  • 6.1.2.1. Fungal mutation in nature
  • 6.2. Natural mutants of fungi
  • 6.2.1. The nature of spontaneous natural mutants in fungi
  • 6.2.2. Gene and chromosomal changes associated with recombination and gene conversion
  • 6.2.3. Mitochondrial mutation in mtDNA: high-frequency specific transfer
  • 6.2.4. Aneuploidy and polyploidy
  • 6.2.5. Mini-chromosomes
  • 6.3. Migration and gene flow
  • 6.3.1. Fungal dispersal in nature: airborne dispersal
  • 6.3.2. Fungal dispersal in nature: dispersal by animals
  • 6.3.3. Establishment of dispersed fungal propagules
  • 6.3.4. Estimating gene flow indirectly
  • Further reading
  • 7. The generation of variation--II The importance and diversity of inbreeding and outbreeding
  • 7.1. Sexual reproduction in nature
  • 7.1.1. The genetic consequences of sexual reproduction
  • 7.2. Mating systems and their variations
  • 7.2.1. Mating systems in Chytridiomycotina
  • 7.2.2. Mating systems in Zygomycotina
  • 7.2.3. Variations on basic mating systems in Ascomycotina
  • 7.2.3.1. Multiple fertilization
  • 7.2.3.2. Inbreeding in normally dimictic Ascomycotina
  • 7.2.3.3. Mating type switching
  • 7.2.3.4. Preferential crossing between siblings
  • 7.2.3.5. Outcrossing in normally self-fertile species
  • 7.2.4. Variations on basic mating systems in Basidiomycotina
  • 7.2.5. Secondary inbreeding: homoheteromixis (secondary homothallism)
  • 7.2.5.1. Homoheteromixis in Ascomycotina
  • 7.2.5.2. Homoheteromixis in Basidiomycotina
  • 7.2.6. Polymorphic and partial sexual expression
  • 7.2 6.1. Female sterility
  • 7.2.7. Sterility
  • 7.2.8. Amixis
  • 7.2.9. Variations on basic mating systems in Straminipila
  • 7.3. The balance of outbreeding and inbreeding
  • 7.3.1.. Environmental effects on sexual reproduction
  • 7.3.2.. More complex in- and outbreeding patterns
  • 7.3.3.. In- and outbreeding: conclusions
  • Appendix. Distinguishing between clones and recombinant populations
  • 7A.1. Direct observation of reproduction in fungi
  • 7A.2. Comparisons of genetic diversity
  • 7A.3. Comparisons of genotypic diversity
  • 7A.4. Gametic disequilibrium
  • 7A.5. The index of association
  • 7A.6. The parsimony tree permutation test
  • 7A.7. Summary
  • Further reading
  • 8. The generation of variation--III Heterokaryosis, parasexuality, hybridization and polyploidy
  • 8.1. Heterokaryosis and parasexuality
  • 8.1.1. Heterokaryosis
  • 8.1.1.1. Heterokaryosis in Mucorales
  • 8.1.1.2. Heterokaryosis in Glomales
  • 8.1.1.3. Heterokaryosis in Ascomycotina and Fungi Anamorphici
  • 8.1.1.4. Heterokaryosis in Basidiomycotina
  • 8.1.2. Parasexuality
  • 8.1.2.1. Parasexuality and the 'Buller phenomenon'
  • 8.1.3. The significance of heterokaryosis and parasexuality for fungi
  • 8.2.. Hybridization and polyploidy
  • 8.2.1. Hybridization in Eumycota
  • 8.2.1.1. Hybridization in species possessing a pheromone in common
  • 8.2.1.2. Hybrids associated with neutral situations
  • 8.2.1.3. Hybridization involving anamorphic forms
  • 8.2.1.4. Other possible hybrids
  • 8.2.2. Hybridization in Straminipila
  • 8.2.3. Polyploidy
  • 8.2.3.1. Polyploidy in Eumycota
  • 8.2.3.2. Polyploidy in Straminipila
  • 8.2.4. The significance of hybridization and polyploidy for fungi
  • Further reading
  • 9. Change in gene frequency in fungal populations--I General considerations: selection for oligogenically determined traits
  • 9.1. General considerations
  • 9.1.1. Quantifying selection and fitness in fungi
  • 9.1.1.1. Oligogenic selection: selection coefficients
  • 9.1.1.2. Multigenic selection: selection differentials
  • 9.2. Special aspects of fungal selection
  • 9.3. Intra-mycelial selection
  • 9.3.1.. Non-nuclear intra-mycelial selection
  • 9.3.1.1. Mycoviruses
  • 9.3.2. Experimental inter-nuclear, intra-mycelial selection in heterokaryons
  • 9.3.3. Inter-nuclear intra-mycelial selection under industrial conditions
  • 9.4. Inter-mycelial selection
  • 9.4.1. Selection for oligogenically determined traits relevant to agricultural situations
  • 9.4.1.1. Selection for fungicide resistance
  • 9.4.1.2. Selection for pathogenicity under agricultural conditions
  • 9.4.1.3. Selection for 'unnecessary' virulence genes: a controversy
  • 9.4.2. Specific virulence genes in wild populations
  • 9.4.3. Density-dependent and frequency-dependent selection
  • 9.4.3.1. Density-dependent selection
  • 9.4.3.2. Frequency-dependent selection
  • Further reading
  • 10. Change in gene frequency in fungal populations--II Natural selection for multigenically determined traits: competition and fitness
  • 10.1. Experimental selection for multigenically determined traits in fungi
  • 10.1.1. Experimental selection for growth rate in fungi
  • 10.1.2. Experimental selection for ascospore size
  • 10.2. Multigenic selection in agricultural situations
  • 10.3. Multigenic selection in natural populations
  • 10.3.1. Selection for quantitative traits in natural populations
  • 10.3.2. Host adaptation
  • 10.3.3. Ecological adaptation
  • 10.3.4. Experimental transplantation as a tool to detect selection
  • 10.4. Intraspecific competition and relative fitness
  • 10.4.1. Experimental studies on intraspecific competition
  • 10.4.2. Field experiments on intraspecific competition
  • 10.5. Complex intraspecific competition in nature
  • 10.6. General comments
  • Appendix. More complex approaches to estimating fitness in fungi
  • 10A.1. Fitness indices
  • 10A.2. More complex analyses of fitness components and selection
  • 10A.2.1. An experiment and a complex fungal model
  • Further reading
  • Part IV. Species and speciation
  • 11. Fungal species
  • 11.1. Fungal species as morphospecies
  • 11.2. Fungal species as agamospecies
  • 11.3. Fungal species as biological species
  • 11.3.1. Biological species and Ascomycotina
  • 11.3.2. Biological species and Basidiomycotina
  • 11.3.3. Biological species in Zygomycotina and Chytridiomycotina
  • 11.3.4. Fungi and the biological species
  • 11.4. Fungi as phylogenetic species
  • 11.5. Conclusions
  • Further reading
  • 12. Speciation in fungi
  • 12.1. Historical aspects of speciation
  • 12.1.1. Taxonomic data and speciation
  • 12.1.2. Assessing species lineages
  • 12.2. Speciation processes
  • 12.2.1. Selection by the habitat
  • 12.2.2. Selection for the timing of development
  • 12.2.3. Episodic selection for adaptive response
  • 12.2.3.1. Dramatic climate change
  • 12.2.3.2. Founder populations, drift and speciation
  • 12.2.3.3. Human influences predisposing to speciation
  • 12.3. Modes of reproductive isolation
  • 12.3.1. The gradual development of reproductive isolation
  • 12.3.2. Abrupt reproductive isolation through change of mating system
  • 12.3.3. Abrupt reproductive isolation through hybridization and polyploidy
  • 12.3.4. 'Instant' speciation--a hypothetical situation
  • 12.4. Fungal populations and speciation
  • 12.4.1. Secondarily asexual species
  • 12.4.2. Sexual fungal species
  • 12.5. Speciation in fungi: some considerations
  • Further reading
  • References
  • Abbreviations
  • Mycological glossary
  • Classification of fungi in the text
  • Species index
  • General index
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