1;Preface;5 2;Contents;6 3;Contributors;8 4;1 Questions and Concepts in Plant Virus Evolution: a Historical Perspective;10 4.1;1.1 Introduction;11 4.2;1.2 The Early Period;11 4.3;1.3 The Analysis of Viral Genomes and Its Impact on Virus Evolution Research: Quasispecies and Phylogenetics;12 4.4;1.4 The Challenge to the Dogma: Viruses Might Be Not So Variable nor Might Their Populations Be So Big;15 4.5;1.5 Recent Times: New Concepts and New Challenges;17 4.6;1.6 Final Comments;19 4.7;References;19 5;2 Community Ecology of Plant Viruses;24 5.1;2.1 Introduction;25 5.2;2.2 Patterns of Host and Vector Specialization;26 5.3;2.3 Virus Interactions Within and Among Hosts;28 5.4;2.4 Virus Spread in a Community Context;29 5.5;2.5 Viruses and Plant Invasions;31 5.6;2.6 Summary;32 5.7;References;33 6;3 Emerging Plant Viruses: a Diversity of Mechanisms and Opportunities;36 6.1;3.1 Introduction;37 6.2;3.2 What are Some Plant Viruses that Presently are Considered as Emergent?;38 6.3;3.3 What Factor(s) Lead to the Emergence of a Plant Virus?;39 6.4;3.4 Reassortment and Recombination: Effective Mechanisms of Variability for DNA Viruses;46 6.5;3.5 Tripartite Begomovirus Complexes: A Way for Bipartite Begomoviruses To Fight Host Defense Responses?;48 6.6;3.6 Acquisition of Novel Viruslike Entities: Monopartite Begomoviruses and their Satellite DNAs;49 6.7;3.7 Emergence of Diseases Caused by Novel Viruslike Agents;51 6.8;3.8 Multiple Mechanisms often Underlie the Emergence of Plant Viruses;51 6.9;3.9 Bringing Them All Together: Tomato Yellow Leaf Curl/ Leaf Curl Disease in West Africa;52 6.10;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 6.11;3.11 Conclusions;56 6.12;References;57 7;4 Evolution of Integrated Plant Viruses;61 7.1;4.1 Introduction;62 7.2;4.2 Plant DNA Viruses;63 7.3;4.3 Detection of Integrated Plant DNA Virus Sequences;65 7.4;4.4 EPRVs Identified in Plant Genomes;67 7.5;4.5 Integration of DNA Copies of RNA Viruses and Viroids;70 7.6;4.6 Evolution;71 7.7;4.7 Conclusions;83 7.8;References;84 8;5 Viroids;90 8.1;5.1 Introduction;91 8.2;5.2 Genome Structure and Replication Strategy;91 8.3;5.3 Evolutionary Relationships Among Subviral RNAs;95 8.4;5.4 Possible Roles of Conserved Sequence Motifs in Viroid Evolution;97 8.5;5.5 Structure of Viroid Quasispecies;98 8.6;5.6 Origin and Evolution of Viroids;109 8.7;5.7 Concluding Remarks;111 8.8;References;112 9;6 Virus Populations, Mutation Rates and Frequencies;116 9.1;6.1 Introduction;117 9.2;6.2 Mutation Sources and Mutagenic Agents;117 9.3;6.3 Quantifying Methods;119 9.4;6.4 Mutational Spectrum;119 9.5;6.5 Mutation Rates Versus Adaptation;120 9.6;6.6 Intrahost Versus Interhost Diversity of Plant Virus Population;121 9.7;6.7 Replication Strategy;122 9.8;6.8 RNA Versus DNA Viruses;123 9.9;6.9 Virus Populations;124 9.10;6.10 Conclusion;124 9.11;References;125 10;7 Genetic Bottlenecks;129 10.1;7.1 Introduction;130 10.2;7.2 Bottlenecks During Systemic Infections;131 10.3;7.3 Bottlenecks During Horizontal Transmission;132 10.4;7.4 Bottlenecks During Vertical Transmission;132 10.5;7.5 Genetic Drift Versus Selection;133 10.6;7.6 Effective Population Size;133 10.7;7.7 Muller's Ratchet in Plant Viruses;134 10.8;7.8 Bottlenecks and Speciation;135 10.9;7.9 Conclusions;135 10.10;References;135 11;8 Recombination in Plant RNA Viruses;138 11.1;8.1 Introduction;139 11.2;8.2 The Benefit of RNA Recombination to RNA Virus Evolution;139 11.3;8.3 The Role of RNA Recombination in Plant Virus Variability;141 11.4;8.4 Experimental Approaches to Study Viral RNA Recombination;143 11.5;8.5 Mechanisms of RNA Recombination;144 11.6;8.6 Classification of RNA Recombinants;145 11.7;8.7 The Role of Viral Replication Proteins in RNA Recombination;148 11.8;8.8 Viral RNA Sequences Form Recombination Hotspots and Coldspots;150 11.9;8.9 The Role of the Host Genes in RNA Recombination;152 11.10;8.10 Conclusions;154 11