McCann Angela, Cotton James A, McInerney James O
Bioinformatics laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co, Kildare, Ireland.
BMC Evol Biol. 2008 Nov 12;8:312. doi: 10.1186/1471-2148-8-312.
In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present.
We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are significantly different to other methods.
We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.
在过去十多年里，重建物种系统发育的重点已从单个基因分析转向多基因乃至完整基因组分析。最简单的扩大规模的方法是在更大规模上使用熟悉的分析方法，这也是最流行的方法。然而，基因的复制和丢失以及水平基因转移（HGT）可能导致基因系统发育和基因组系统发育之间仅存在间接关系的情况。在本研究中，我们检验了五种广泛使用的方法及其变体，以查看它们是否实际上或多或少表达相同的内容。特别是，我们重点关注条件重建，因为即使存在水平基因转移，该方法也被设计为能良好运行。
我们证实了之前的一个观点，即该方法存在系统偏差。我们表明，没有两种方法会产生相同的结果，并且目前大多数推断基因组系统发育的方法所产生的结果与其他方法显著不同。
我们得出结论，基因组系统发育需要根据用于构建它们的方法进行不同的解释。
