Preface	5
	Contents	6
	Contributors	8
	1 Questions and Concepts in Plant Virus Evolution: a Historical Perspective	10
	1.1 Introduction	11
	1.2 The Early Period	11
	1.3 The Analysis of Viral Genomes and Its Impact on Virus Evolution Research: Quasispecies and Phylogenetics	12
	1.4 The Challenge to the Dogma: Viruses Might Be Not So Variable nor Might Their Populations Be So Big	15
	1.5 Recent Times: New Concepts and New Challenges	17
	1.6 Final Comments	19
	References	19
	2 Community Ecology of Plant Viruses	24
	2.1 Introduction	25
	2.2 Patterns of Host and Vector Specialization	26
	2.3 Virus Interactions Within and Among Hosts	28
	2.4 Virus Spread in a Community Context	29
	2.5 Viruses and Plant Invasions	31
	2.6 Summary	32
	References	33
	3 Emerging Plant Viruses: a Diversity of Mechanisms and Opportunities	36
	3.1 Introduction	37
	3.2 What are Some Plant Viruses that Presently are Considered as Emergent?	38
	3.3 What Factor(s) Lead to the Emergence of a Plant Virus?	39
	3.4 Reassortment and Recombination: Effective Mechanisms of Variability for DNA Viruses	46
	3.5 Tripartite Begomovirus Complexes: A Way for Bipartite Begomoviruses To Fight Host Defense Responses?	48
	3.6 Acquisition of Novel Viruslike Entities: Monopartite Begomoviruses and their Satellite DNAs	49
	3.7 Emergence of Diseases Caused by Novel Viruslike Agents	51
	3.8 Multiple Mechanisms often Underlie the Emergence of Plant Viruses	51
	3.9 Bringing Them All Together: Tomato Yellow Leaf Curl/ Leaf Curl Disease in West Africa	52
	3.10 Emergence of a New Virus is not always Catastrophic: Failure of New Viral Diseases to Emerge Following a Major Change in the Whitefly Vector Population	53
	3.11 Conclusions	56
	References	57
	4 Evolution of Integrated Plant Viruses	61
	4.1 Introduction	62
	4.2 Plant DNA Viruses	63
	4.3 Detection of Integrated Plant DNA Virus Sequences	65
	4.4 EPRVs Identified in Plant Genomes	67
	4.5 Integration of DNA Copies of RNA Viruses and Viroids	70
	4.6 Evolution	71
	4.7 Conclusions	83
	References	84
	5 Viroids	90
	5.1 Introduction	91
	5.2 Genome Structure and Replication Strategy	91
	5.3 Evolutionary Relationships Among Subviral RNAs	95
	5.4 Possible Roles of Conserved Sequence Motifs in Viroid Evolution	97
	5.5 Structure of Viroid Quasispecies	98
	5.6 Origin and Evolution of Viroids	109
	5.7 Concluding Remarks	111
	References	112
	6 Virus Populations, Mutation Rates and Frequencies	116
	6.1 Introduction	117
	6.2 Mutation Sources and Mutagenic Agents	117
	6.3 Quantifying Methods	119
	6.4 Mutational Spectrum	119
	6.5 Mutation Rates Versus Adaptation	120
	6.6 Intrahost Versus Interhost Diversity of Plant Virus Population	121
	6.7 Replication Strategy	122
	6.8 RNA Versus DNA Viruses	123
	6.9 Virus Populations	124
	6.10 Conclusion	124
	References	125
	7 Genetic Bottlenecks	129
	7.1 Introduction	130
	7.2 Bottlenecks During Systemic Infections	131
	7.3 Bottlenecks During Horizontal Transmission	132
	7.4 Bottlenecks During Vertical Transmission	132
	7.5 Genetic Drift Versus Selection	133
	7.6 Effective Population Size	133
	7.7 Muller’s Ratchet in Plant Viruses	134
	7.8 Bottlenecks and Speciation	135
	7.9 Conclusions	135
	References	135
	8 Recombination in Plant RNA Viruses	138
	8.1 Introduction	139
	8.2 The Benefit of RNA Recombination to RNA Virus Evolution	139
	8.3 The Role of RNA Recombination in Plant Virus Variability	141
	8.4 Experimental Approaches to Study Viral RNA Recombination	143
	8.5 Mechanisms of RNA Recombination	144
	8.6 Classification of RNA Recombinants	145
	8.7 The Role of Viral Replication Proteins in RNA Recombination	148
	8.8 Viral RNA Sequences Form Recombination Hotspots and Coldspots	150
	8.9 The Role of the Host Genes in RNA Recombination	152
	8.10 Conclusions	154
	References	155
	9 Symbiosis, Mutualism and Symbiogenesis	162
	9.1 Introduction	162
	9.2 Virus–Host Symbiosis	163
	9.3 Virus–Host Symbiogenesis	164
	9.4 Virus–Virus Symbiosis	164
	9.5 Virus–Virus Symbiogenesis	165
	9.6 Conclusions	166
	References	166
	10 Methods for Analyzing Viral Evolution	170
	10.1 Introduction	171
	10.2 Alignment Strategies	171
	10.3 Model Selection: Beyond Kimura 2-Parameter	176
	10.4 Phylogenetic Inference: Picking Trees from the Forest	181
	10.5 Population Inference	188
	10.6 Summary	200
	References	200
	11 Virus Evolution and Taxonomy	210
	11.1 Brief Overview of Virus Taxonomy	211
	11.2 Elements Dictating Taxonomy	211
	11.3 Taxonomy and Evolution	212
	11.4 The Problems of Plant Virus Taxonomy	215
	11.5 Concluding Remarks	219
	References	221
	Index	223