Fungal Populations and Species

by Burnett, John

• ISBN13: 9780198515524
• ISBN10: 0198515529
• Format: Hardcover
• Copyright: 2003-03-13
• Publisher: Oxford University Press

Summary

The population genetics and speciation of fungi is a rapidly developing field, heavily dependent upon the use of molecular markers. No basic text exists which describes the methods employed or the findings obtained from such investigations. This book is intended to provide such an account. Itdescribes the methodologies employed and, for the benefit of the non-mycological reader, a brief introduction to basic fungal biology. Recent findingsrelating to processes in fungal populations - mutation, migration, recombination, heterokaryosis, hybridization, polyploidy, and the operation of selective forces are combined with traditional fungal biology. Finally the taxonomic problems raised by fungal species are discussed, together with theprocesses of speciation.

Table of Contents

Introduction	1	(2)
PART I Basic mycology	3	(24)
Elements of classification, structure, sexuality, biology and genetics of Fungi	5	(22)
Elements of classification	5	(3)
Convention on the use of names in mycology	6	(2)
Life cycles	8	(1)
Structural considerations	9	(4)
Hyphae and mycelia	9	(2)
Dimorphism	11	(1)
Perennating structures	11	(1)
Spores and conidia	12	(1)
Sexual reproduction and sexuality	13	(5)
Mating systems	16	(2)
Dispersal	18	(1)
Aspects of fungal biology of genetic significance	19	(5)
Clones	20	(1)
Phenotypic plasticity	20	(1)
Pleomorphism	21	(1)
Heterokaryosis and the parasexual cycle	21	(1)
Chromosomal DNA and cytology	22	(1)
Cytoplasmic organelles and other inherited cytoplasmic components	23	(1)
A simplified classification of the fungi	24	(3)
Further reading	25	(2)
PART II Methodology	27	(76)
Genetic markers for population studies---I Morphological, physiological and cytological markers	29	(18)
Morphological markers	30	(1)
Mating-type factors	30	(1)
Somatic incompatibility (SI)	31	(8)
SI in Ascomycotina and Fungi Anamorphici	31	(1)
Recognizing SI in Ascomycotina	32	(1)
Heterokaryon self-incompatibility	33	(1)
SI in similar or related taxa	33	(1)
SI genetics	34	(1)
Complex SI behaviour	35	(1)
SI in Basidiomycotina	35	(2)
Recognizing SI in Basidiomycotina	37	(1)
Complex SI	38	(1)
Monokaryotic homogenic incompatibility in Basidiomycotina	38	(1)
Spatial extent of SI genets	39	(1)
SI genetics	39	(1)
Pathogenic markers	39	(2)
Virulence characters	39	(1)
Virulence genetics	40	(1)
Aggressiveness	41	(1)
Fungicide resistance as a marker	41	(1)
Cytological markers	42	(5)
Chromosomal techniques	42	(1)
Electrophoretic chromosomal techniques	43	(2)
Karyotyping procedures	45	(1)
Further reading	45	(2)
Genetic markers for population studies---II Molecular markers	47	(18)
Specific molecules	47	(1)
Proteins and polymorphic enzymes	48	(2)
Nucleic acids	50	(13)
The use of whole DNA molecules	52	(1)
The polymerase chain reaction	53	(1)
Primers for PCR	54	(1)
Random amplified polymorphic DNA (RAPD)	55	(1)
Template-mixed RAPDs	55	(1)
Sequence-characterized amplified regions (SCARs)	56	(1)
RAPD with single-strand conformational polymorphism (RAPD--SSCP or SSCP)	56	(1)
Denaturing gradient gel electrophoresis (DGGE or CDGE)	56	(1)
Variable numbers of tandem repeats (VNTRs)	56	(1)
Simple sequence repeats or microsatellites (SSRs)	57	(1)
Random amplified microsatellites (RAMs)	57	(1)
Amplified fragment-length polymorphism (AFLPs)	58	(1)
The analysis of nucleotide fragments	59	(1)
Sequencing	59	(1)
Restriction fragment length polymorphisms (RFLPs)	60	(1)
The use of probes with RFLPs: Southern blots	61	(1)
Amplified fragments	62	(1)
The utility of different molecular screening techniques	63	(1)
Taxonomic identification using sequence markers	63	(2)
Further reading	64	(1)
Defining fungal individuals: ecological, biological and genetical aspects; sampling	65	(15)
The physical and biological attributes of fungal genets	66	(4)
Mycelial extent	67	(1)
Substrate specificity and specific site locations	68	(1)
Persistence	68	(2)
Propagule dispersal and cloning	70	(1)
Recognition of intraspecific groups, genets and fungal individuals	70	(3)
Using the SI reaction	71	(1)
Using pathogenicity characters	72	(1)
Using molecular markers	72	(1)
Summation	73	(1)
Sampling	73	(7)
Spatial sampling procedures	74	(1)
Site sampling	74	(3)
Sample size	77	(1)
Pattern recognition	77	(2)
Practical techniques for isolating and recognizing fungi	79	(1)
Further reading	79	(1)
Describing and analysing populations: basic genetic and phylogenetic aspects	80	(23)
Phenotypic and genetic diversity	81	(6)
Phenotypic diversity	81	(2)
Phenotypic similarity and dissimilarity	83	(1)
Similarity	83	(1)
Dissimilarity	84	(1)
Genetic and genotypic diversity	84	(1)
Comparing genetic variation within subdivided populations or between populations	85	(2)
Character association: the recognition of distinct genotypic groups and their relationships	87	(9)
ANOVA and AMOVA	89	(1)
Ordination methods	90	(2)
Hierarchical methods	92	(1)
Distance methods	93	(1)
Discrete character methods	94	(1)
Estimating the likelihood of any tree and discriminating between alternative trees	95	(1)
Population history: the coalescent and nested clade analysis	96	(7)
Further reading	101	(2)
PART III Processes in populations	103	(136)
The generation of variation---I Mutation and migration	105	(25)
The establishment of mutants, random genetic change and the frequency of detectable mutations	105	(7)
Genetic hitch-hiking	109	(1)
The frequency of mutation in fungal chromosomes	109	(1)
Fungal mutation in nature	110	(2)
Natural mutants of fungi	112	(7)
The nature of spontaneous natural mutants in fungi	112	(2)
Gene and chromosomal changes associated with recombination and gene conversion	114	(3)
Mitochondrial mutation in mtDNA: high-frequency specific transfer	117	(1)
Aneuploidy and polyploidy	118	(1)
Mini-chromosomes	119	(1)
Migration and gene flow	119	(11)
Fungal dispersal in nature: airborne dispersal	120	(5)
Fungal dispersal in nature: dispersal by animals	125	(1)
Establishment of dispersed fungal propagules	125	(1)
Estimating gene flow indirectly	126	(2)
Further reading	128	(2)
The generation of variation---II The importance and diversity of inbreeding and outbreeding	130	(32)
Sexual reproduction in nature	131	(4)
The genetic consequences of sexual reproduction	132	(3)
Mating systems and their variations	135	(14)
Mating systems in Chytridiomycotina	136	(1)
Mating systems in Zygomycotina	137	(1)
Variations on basic mating systems in Ascomycotina	138	(1)
Multiple fertilization	138	(1)
Inbreeding in normally dimictic Ascomycotina	139	(1)
Mating type switching	139	(1)
Preferential crossing between siblings	140	(1)
Outcrossing in normally self-fertile species	140	(1)
Variations on basic mating systems in Basidiomycotina	141	(1)
Secondary inbreeding: homoheteromixis (secondary homothallism)	142	(1)
Homoheteromixis in Ascomycotina	142	(1)
Homoheteromixis in Basidiomycotina	143	(2)
Polymorphic and partial sexual expression	145	(1)
Female sterility	145	(2)
Sterility	147	(1)
Amixis	147	(1)
Variations on basic mating systems in Straminipila	148	(1)
The balance of outbreeding and inbreeding	149	(13)
Environmental effects on sexual reproduction	149	(2)
More complex in- and outbreeding patterns	151	(2)
In- and outbreeding: conclusions	153	(1)
Appendix: Distinguishing between clones and recombinant populations	153	(2)
Direct observation of reproduction in fungi	155	(1)
Comparisons of genetic diversity	156	(1)
Comparisons of genotypic diversity	156	(1)
Gametic disequilibrium	157	(2)
The index of association	159	(1)
The parsimony tree permutation test	160	(1)
Summary	161	(1)
Further reading	161	(1)
The generation of variation---III Heterokaryosis, parasexuality, hybridization and polyploidy	162	(23)
Heterokaryosis and parasexuality	162	(9)
Heterokaryosis	164	(1)
Heterokaryosis in Mucorales	164	(1)
Heterokaryosis in Glomales	164	(3)
Heterokaryosis in Ascomycotina and Fungi Anamorphici	167	(1)
Heterokaryosis in Basidiomycotina	168	(1)
Parasexuality	169	(1)
Parasexuality and the 'Buller phenomenon'	170	(1)
The significance of heterokaryosis and parasexuality for fungi	171	(1)
Hybridization and polyploidy	171	(14)
Hybridization in Eumycota	172	(1)
Hybridization in species possessing a pheromone in common	172	(3)
Hybrids associated with neutral situations	175	(3)
Hybridization involving anamorphic forms	178	(2)
Other possible hybrids	180	(1)
Hybridization in Straminipila	181	(1)
Polyploidy	182	(1)
Polyploidy in Eumycota	182	(1)
Polyploidy in Straminipila	183	(1)
The significance of hybridization and polyploidy for fungi	184	(1)
Further reading	184	(1)
Change in gene frequency in fungal populations---I General considerations: selection for oligogenically determined traits	185	(23)
General considerations	185	(6)
Quantifying selection and fitness in fungi	188	(1)
Oligogenic selection: selection coefficients	188	(2)
Multigenic selection: selection differentials	190	(1)
Special aspects of fungal selection	191	(1)
Intra-mycelial selection	191	(7)
Non-nuclear intra-mycelial selection	192	(1)
Mycoviruses	192	(1)
Experimental inter-nuclear, intra-mycelial selection in heterokaryons	192	(3)
Inter-nuclear intra-mycelial selection under industrial conditions	195	(3)
Inter-mycelial selection	198	(10)
Selection for oligogenically determined traits relevant to agricultural situations	198	(1)
Selection for fungicide resistance	198	(1)
Selection for pathogenicity under agricultural conditions	199	(2)
Selection for 'unnecessary' virulence genes: a controversy	201	(2)
Specific virulence genes in wild populations	203	(2)
Density-dependent and frequency-dependent selection	205	(1)
Density-dependent selection	205	(1)
Frequency-dependent selection	206	(1)
Further reading	207	(1)
Change in gene frequency in fungal populations---II Natural selection for multigenically determined traits: competition and fitness	208	(31)
Experimental selection for multigenically determined traits in fungi	208	(3)
Experimental selection for growth rate in fungi	208	(3)
Experimental selection for ascospore size	211	(1)
Multigenic selection in agricultural situations	211	(1)
Multigenic selection in natural populations	212	(10)
Selection for quantitative traits in natural populations	213	(1)
Host adaptation	213	(4)
Ecological adaptation	217	(3)
Experimental transplantation as a tool to detect selection	220	(2)
Intraspecific competition and relative fitness	222	(4)
Experimental studies on intraspecific competition	223	(2)
Field experiments on intraspecific competition	225	(1)
Complex intraspecific competition in nature	226	(1)
General comments	227	(12)
Appendix: More complex approaches to estimating fitness in fungi	230	(1)
Fitness indices	230	(1)
More complex analyses of fitness components and selection	231	(3)
An experiment and a complex fungal model	234	(4)
Further reading	238	(1)
PART IV Species and speciation	239	(53)
Fungal species	241	(22)
Fungal species as morphospecies	242	(2)
Fungal species as agamospecies	244	(3)
Fungal species as biological species
Biological species and Ascomycotina	247	(2)
Biological species and Basidiomycotina	249	(5)
Biological species in Zygomycotina and Chytridiomycotina	254	(1)
Fungi and the biological species	255	(1)
Fungi as phylogenetic species	256	(5)
Conclusions	261	(2)
Further reading	262	(1)
Speciation in fungi	263	(29)
Historical aspects of speciation	263	(4)
Taxonomic data and speciation	264	(1)
Assessing species lineages	264	(3)
Speciation processes	267	(9)
Selection by the habitat	269	(2)
Selection for the timing of development	271	(1)
Episodic selection for adaptive response	272	(1)
Dramatic climate change	272	(1)
Founder populations, drift and speciation	273	(1)
Human influences predisposing to speciation	273	(3)
Modes of reproductive isolation	276	(10)
The gradual development of reproductive isolation	277	(3)
Abrupt reproductive isolation through change of mating system	280	(3)
Abrupt reproductive isolation through hybridization and polyploidy	283	(1)
`Instant' speciation---a hypothetical situation	284	(2)
Fungal populations and speciation	286	(4)
Secondarily asexual species	286	(2)
Sexual fungal species	288	(2)
Speciation in fungi: some considerations	290	(2)
Further reading	290	(2)
References	292	(36)
Abbreviations	328	(1)
Mycological glossary	329	(4)
Classification of fungi in the text	333	(4)
Species index	337	(5)
General index	342