Experimental Phylogenies Using Viruses for Testing Phylogenetic Methods

生物学家一直对重建 有许多程序已经被用来 提供这样的重建。 然而，几乎没有 其中的例子，其中的遗传学是已知的，提前， 可以直接测试重建方法。 在本研究中， 病毒（T7噬菌体）将在实验室中培养， 存在诱变剂以产生已知的诱变剂，DNA序列 信息将从所产生的血统中获得，而这些 数据将被用来测试重建遗传学的方法。 实验将考虑（i）树的形状的影响 （分支结构和分支长度）对 重建方法，（ii）分子环境的影响 收敛，和（iii）恒定的分子变化率。 的 收集的数据将是DNA序列和限制酶切割 病毒基因组的位点。 这项研究将影响该领域 系统生物学在建立经验方法论 为实验性的生物工程建设和提供直接的 系统发育推断方法的测试。 这些系统发育 方法对许多领域变得越来越重要， 生物学 初步数据已经收集，以证明这两个 研究的技术可行性和 系统为这些目标。

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.