Biologists have long been interested in reconstructing the history of life, and there are many procedures that have been used to provide such reconstructions. However, there are almost no examples in which the phylogeny is known in advance, whereby the reconstruction methods can be tested directly. In this study, viruses (T7 bacteriophage) will be grown in the laboratory in the presence of a mutagen to generate known phylogenies, DNA sequence information will be obtained from the resultant lineages, and these data will be used to test methods of phylogeny reconstruction. Experiments will consider (i) the effect of the shape of the tree (branching structure and branch lengths) on the accuracy of reconstruction methods, (ii) the effect of environment of molecular convergence, and (iii) constancy of rates of molecular change. The data gathered will be DNA sequences and restriction enzyme cleavage sites of the viral genome. This study will impact the field of systematic biology both in establishing an empirical methodology for experimental phylogeny construction and in providing direct tests of phylogenetic inference methodology. These phylogenetic methods have become increasingly important to many fields of biology. Preliminary data have been collected to demonstrate both the technical feasibility of the study and the utility of the system for these objectives.
