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

BMC Evolutionary Biology. 2008;8(1):312 DOI 10.1186/1471-2148-8-312

 

Journal Homepage

Journal Title: BMC Evolutionary Biology

ISSN: 1471-2148 (Online)

Publisher: BMC

LCC Subject Category: Science: Biology (General): Evolution

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

McInerney James O
Cotton James A
McCann Angela

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 17 weeks

 

Abstract | Full Text

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.</p>