Puigbò Pere, Wolf Yuri I, Koonin Eugene V
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Methods Mol Biol. 2012;856:53-79. doi: 10.1007/978-1-61779-585-5_3.
Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."
系统发育树的全基因组比较正日益成为进化基因组学中一种常见的方法，并且已经开发出了多种用于此类比较的方法。在本文中，我们介绍了几种用于大量系统发育树比较分析的方法。为了在考虑每个内部分支的自展支持率的情况下比较系统发育树，我们引入了Boot-Split距离（BSD）方法，作为先前开发的用于树比较的分裂距离方法的扩展。BSD方法实现了一个直接的想法，即通过根据自展支持率对树的分裂进行不同处理，可以使系统发育树的比较更加稳健。我们还介绍了一些方法，用于检测生命系统发育森林（FOL）中的树状和网状进化趋势，即原核生物保守基因的所有系统发育树。为此目的所采用的主要方法包括将物种四重奏映射到树上，以计算每个四重奏拓扑结构的支持率，从而量化树状和网状结构对物种间距离的贡献。我们描述了这些方法在分析FOL中的应用以及使用这些方法获得的结果。这些结果支持了生命之树（TOL）作为FOL中的核心进化趋势这一概念，这与传统上将TOL视为“物种树”的观点相反。
