Methods for analyzing viral evolution

Abstract

Phylogenetic approaches are central to the study of plant virus evolution and coevolution with plant hosts. Phylogenetics is a field that is rapidly advancing and spans the population/species boundary to include examining relationships among species as well as population dynamics and genetic associations within species. With a strong phylogenetic framework, a variety of exciting questions can be addressed relative to the evolutionary history of plant viruses. In this chapter, we outline the basic approaches for estimating phylogenetic or evolutionary histories for a set of genetic sequences and then explore a variety of approaches to test hypotheses concerning viral population dynamics, selection pressures, recombination, genetic diversity, and population growth. © 2008 Springer Berlin Heidelberg.