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MBE Advance Access published online on November 9, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj061
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted November 2, 2005

Research Article

Improved Consensus Network Techniques for Genome-Scale Phylogeny

Barbara R. Holland 1*, Lars S. Jermiin 2, and Vincent Moulton 3

1 Allan Wilson Centre, Institute of Fundamental Sciences, Massey University, New Zealand
2 School of Biological Sciences and Sydney University Biological Informatics & Technology Centre, University of Sydney, NSW 2006, Australia; Unité de Biologie Moleculaire de Gène chez les Extrêmophiles, Institute Pasteur, 75724 Paris Cedex 15, France
3 School of Computing Sciences, University of East Anglia, NR4 7TJ, UK

* To whom correspondence should be addressed.
Barbara R. Holland, E-mail: b.r.holland{at}massey.ac.nz


  Abstract

Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces stochastic error, the potential for systematic error still remains, heightening the need for reliable methods to analyse multi-gene data sets. Consensus methods provide an alternative, more inclusive, approach for analysing collections of trees arising from multiple genes. We extend a previously described consensus network method for genome-scale phylogeny (Molecular Biology and Evolution 21, 1459-1461) to incorporate additional information. This additional information could come from bootstrap analysis, Bayesian analysis, or various methods to find confidence sets of trees. The new methods can be extended to include edge weights representing genetic distance. We use three data sets to illustrate the approach: 61 genes from 14 angiosperm taxa and one gymnosperm, 106 genes from eight yeast taxa, and 46 members of a gene family from 15 vertebrate taxa.

Keywords: consensus networks; genome-scale phylogeny; gene trees.
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[Abstract] [Full Text] [PDF]


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