It appears that one of the first things that occurred to Felix d'Herelle when he discovered bacteriophages in 1917 was that these mysterious objects might provide a means of killing bacteria that are pathogenic to humans (Summers, 1999). The still ongoing story of phage therapy, as this approach was called, has been told elsewhere and will not be retold here, but it serves to point out that scientists have been interested in the effects of phages on their hosts since their discovery. d'Herelle believed, and eventually established, that phages are viruses that infect bacteria. However, it was not until the experimental investigations of phages at the dawn of molecular biology in the 1940s and 1950s that it became clear that phages - and for that matter their bacterial hosts - are genetic organisms (Luria and Delbrück, 1943; Hershey and Rotman, 1949; Hershey and Chase, 1952; Stent, 1963), just like fruit flies, corn, and humans, and so could be expected to mutate and evolve.
Although some work was done on the evolution of phages in the 1960s, 1970s, and 1980s, a more detailed understanding of the genetic mechanisms of phage evolution had to wait until the advent of high-throughput DNA sequencing in the 1990s. This is because the genetic history of a phage, while it is to a significant extent encoded in the phage's genome sequence, is largely invisible to our analysis until we can compare that sequence to the genome sequences of other phages.
Bacteriophages have a long history as objects of biological study. They were discovered about 90 years ago and have engaged biologists ever since, initially for their potential in combating human disease through phage therapy. Later, phages served as arguably the most important model systems in the development of the discipline of molecular biology and the associated explosion of knowledge about the detailed workings of genes and cells. Yet it is only in very recent years that the study of phage evolution has attracted the attention of more than a handful of individuals. The primary reasons for the current increased interest in phage evolution, I would suggest, are two: discovery, over the past 20 years, of astonishingly high phage population numbers in the natural environment, and improved, low-cost methods of phage genotypic analysis, especially DNA sequencing. In this chapter I discuss the abundance and diversity of the global phage population, with an emphasis on what we are learning from comparative genomic studies about the mechanisms by which it has evolved to its current state.
Chapter 6 provides an introduction to basic evolutionary mechanisms of phage evolution. See Hendrix (2003), Casjens (2005), and Brüssow and Desiere (2006) for additional reviews of phage evolution from the perspective of genomic studies.
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