Experimental Phylogenies Using Viruses for Testing Phylogenetic Methods

生物学家长期以来一直对重建生命历史感兴趣，有许多程序被用来提供这种重建。然而，几乎没有预先知道系统发展史的例子，从而可以直接测试重建方法。在这项研究中，病毒(T7噬菌体)将在实验室中培养，在诱变剂存在的情况下产生已知的系统发生，将从得到的谱系中获得DNA序列信息，这些数据将用于测试系统发生重建的方法。实验将考虑(I)树的形状(分支结构和分支长度)对重建方法的准确性的影响，(Ii)分子收敛环境的影响，以及(Iii)分子变化速率的稳定性。收集的数据将是病毒基因组的DNA序列和限制性内切酶切割位点。这项研究将对系统生物学领域产生影响，既为实验系统发生学构建建立经验方法论，也为系统发育推断方法论提供直接测试。这些系统发育方法对生物学的许多领域变得越来越重要。已经收集了初步数据，以证明这项研究的技术可行性和该系统对这些目标的实用性。

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.