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

McCann, A., Cotton, J. A. and McInerney, J. O. (2008) The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. BMC Evolutionary Biology, 8, 312. (doi: 10.1186/1471-2148-8-312) (PMID:19014489) (PMCID:PMC2592249)

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Cotton, Professor James
• Authors: McCann, A., Cotton, J. A., and McInerney, J. O.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: BMC Evolutionary Biology
• Publisher: BioMed Central
• ISSN: 1471-2148
• ISSN (Online): 1471-2148
• Copyright Holders: Copyright © 2008 McCann et al.
• First Published: First published in BMC Evolutionary Biology 8: 312
• Publisher Policy: Reproduced under a Creative Commons License