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Originally published as Genetics Published Articles Ahead of Print on January 31, 2005.

Genetics, Vol. 170, 19-31, May 2005, Copyright © 2005
doi:10.1534/genetics.104.034488

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Adaptive Molecular Evolution for 13,000 Phage Generations

A Possible Arms Race

Holly A. Wichman*,1, Jack Millstein* and J. J. Bull{dagger}

* Department of Biological Sciences and Initiative for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844-3051
{dagger} Department of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712-1023

1 Corresponding author: Department of Biological Sciences, P.O. Box 443051, University of Idaho, Moscow, ID 83844-3051.
E-mail: hwichman{at}uidaho.edu

Bacteriophage {phi}X174 was evolved on a continuous supply of sensitive hosts for 180 days (~13,000 phage generations). The average rate of nucleotide substitution was nearly 0.2% (11 substitutions)/20 days, and, surprisingly, substitutions accumulated in a clock-like manner throughout the study, except for a low rate during the first 20 days. Rates of silent and missense substitutions varied over time and among genes. Approximately 40% of the 71 missense changes and 25% of the 58 silent changes have been observed in previous adaptations; the rate of parallel substitution was highest in the early phase of the evolution, but 7% of the later changes had evolved in previous studies of much shorter duration. Several lines of evidence suggest that most of the changes were adaptive, even many of the silent substitutions. The sustained, high rate of adaptive evolution for 180 days defies a model of adaptation to a constant environment. We instead suggest that continuing molecular evolution reflects a potentially indefinite arms race, stemming from high levels of co-infection and the resulting conflict among genomes competing within the same cell.




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