Bininda-Emonds Olaf R P
Lehrstuhl für Tierzucht, Technical University of Munich, 85354 Freising-Weihenstephan, Germany.
Methods Enzymol. 2005;395:745-57. doi: 10.1016/S0076-6879(05)95038-6.
Supertree construction is the process whereby overlapping phylogenetic trees, and not character data, are combined to yield a larger, more comprehensive phylogeny. In this chapter, I review the logic and methodology behind supertree construction and argue that it holds a necessary place in phylogenetic inference. Much of the justification for supertrees is admittedly practical. As I show with an empirical example, most large groups have insufficient sequence data to build complete phylogenies for them. By being able to indirectly combine diverse forms of phylogenetic information, supertrees are the best method for constructing complete phylogenies of groups with hundreds of species. However, supertree construction can also be justified on theoretical grounds. As whole genomic data are obtained for increasing numbers of species, the theoretical and practical advantages of supertrees together will ensure that the method will play a necessary analytical role as part of a divide-and-conquer strategy to reconstructing the Tree of Life.
超树构建是一个将重叠的系统发育树（而非性状数据）进行合并以产生更大、更全面的系统发育关系的过程。在本章中，我回顾了超树构建背后的逻辑和方法，并认为它在系统发育推断中占有必要的地位。诚然，超树构建的许多理由都是基于实际情况。正如我通过一个实证例子所展示的，大多数大的类群没有足够的序列数据来为它们构建完整的系统发育树。通过能够间接整合各种形式的系统发育信息，超树是构建包含数百个物种的类群的完整系统发育树的最佳方法。然而，超树构建也可以从理论角度得到论证。随着越来越多物种的全基因组数据被获取，超树构建在理论和实际方面的优势将共同确保该方法作为重建生命之树的分而治之策略的一部分发挥必要的分析作用。
