EXPERIMENTAL MOLECULAR EVOLUTION OF BACTERIOPHAGE-T7

We present an analysis of molecular evolution in a laboratory-generate d phylogeny of the bacteriophage T7, a virus of 40 kilo-base pairs of double-stranded DNA. The known biology of T7 is used in concert with o bserved changes in restriction sites and in DNA sequences to produce a model of restriction-site convergence and divergence in the experimen tal lineages. During laboratory propagation in the presence of a mutag en, the phage lineages changed an estimated 0.5%- 1.5% in base pairs; most change appears to have been G --> A or C --> T, presumably becaus e of the mutagen employed. Some classes of restriction-site losses can be explained adequately as simple outcomes of random processes, given the mutation rate and the bias in mutation spectrum. However, some ot her classes of sites appear to have undergone accelerated rates of los s, as though the losses were selectively favored. Overall, the wealth of knowledge available for T7 biology contributes only modestly to the se explanations of restriction-site evolution, but rates of restrictio n-site gains remain poorly explained, perhaps requiring an even deeper understanding of T7 genetics than was employed here. Having measured these properties of molecular evolution, we programmed computer simula tions with the parameter estimates and pseudo-replicated the empirical study, thereby providing a data base for statistical evaluation of ph ylogeny reconstruction methods. By these criteria, replicates of the e xperimental phylogeny would be correctly reconstructed over 97% of the time for the three methods tested, but the methods differed significa ntly both in their ability to recover the correct topology and in thei r ability to predict branch lengths. More generally, the study illustr ates how analyses of experimental evolution in bacteriophage can be ex ploited to reveal relationships between the basics of molecular evolut ion and abstract models of evolutionary processes.