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
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: |
|
| Use Licence: |
This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available
here |
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