The evolution of viruses has been a topic of intense investigation and theoretical development over the past several decades. Numerous workshops, review articles, and books have been devoted to the subject. Medical practitioners have recognized the importance of viral evolution when treating patients with viral diseases. Farmers have recognized the importance of understanding virus evolution in combating emerging viral diseases in their crop plants. As with any field where knowledge is rapidly expanding, many controversies have also arisen about the nature of virus evolution, how to describe virus populations, how to analyze sequence data and estimate phylogenies, etc. Differing points of view will also be found in the various chapters of this book, and I leave it to the readers to decide for themselves which side they find most helpful. In some cases it seems to me that all sides are correct. In other cases, future historians will decide. This book focuses on the evolution of plant viruses, although some chapters also draw on the more extensive knowledge of animal viruses. It covers topics on evo- tionary mechanisms, viral ecology and emergence, appropriate methods for analysis, and the role of evolution in taxonomy. It includes RNA viruses, DNA viruses, integrated viruses and viroids.

Questions and Concepts in Plant Virus Evolution: a Historical Perspective

Community Ecology of Plant Viruses
Emerging Plant Viruses: a Diversity of Mechanisms and Opportunities
Evolution of Integrated Plant Viruses
Viroids
Virus Populations, Mutation Rates and Frequencies
Genetic Bottlenecks
Recombination in Plant RNA Viruses
Symbiosis, Mutualism and Symbiogenesis
Methods for Analyzing Viral Evolution
Virus Evolution and Taxonomy.