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BMC Evol Biol. 2008 Nov 12;8:312. doi: 10.1186/1471-2148-8-312.

The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.

Author information

  • 1Bioinformatics laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co, Kildare, Ireland. angela.mccann@nuim.ie

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSION:

We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.

PMID:
19014489
[PubMed - indexed for MEDLINE]
PMCID:
PMC2592249
Free PMC Article
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