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


    McCann, Angela and Cotton, James A. and McInerney, James O. (2008) The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods. BMC Evolutionary Biology, 8 (312). pp. 1-3. ISSN 1471-2148

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    Official URL: http://www.biomedcentral.com/1471-2148/8/312


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    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: Article
    Additional Information: © 2008 McCann et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    Keywords: tree of genomes; genome-phylogeny; reconstruction methods; horizontal gene transfer;
    Academic Unit: Faculty of Science and Engineering > Biology
    Item ID: 6263
    Identification Number: https://doi.org/10.1186/1471-2148-8-312
    Depositing User: Dr. James McInerney
    Date Deposited: 17 Jul 2015 11:08
    Journal or Publication Title: BMC Evolutionary Biology
    Publisher: BioMed Central
    Refereed: Yes
    Funders: Science Foundation Ireland (SFI), Irish Research Council for Science Engineering and Technology (IRCSET)
    URI:

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