MBE Advance Access originally published online on November 9, 2005
Molecular Biology and Evolution 2006 23(5):848-855; doi:10.1093/molbev/msj061
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Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005 |
Improved Consensus Network Techniques for Genome-Scale Phylogeny
* Allan Wilson Centre, Institute of Fundamental Sciences, Massey University, New Zealand; School of Biological Sciences and Sydney University Biological Informatics & Technology Centre, University of Sydney, Sydney, Australia; Unité de Biologie Moleculaire de Gène chez les Extrêmophiles, Institut Pasteur, Paris, France; and School of Computing Sciences, University of East Anglia, Norwich, United Kingdom
E-mail: b.r.holland{at}massey.ac.nz.
Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces the stochastic error, the potential for systematic error still remains, heightening the need for reliable methods to analyze multigene data sets. Consensus methods provide an alternative, more inclusive, approach for analyzing collections of trees arising from multiple genes. We extend a previously described consensus network method for genome-scale phylogeny (Holland, B. R., K. T. Huber, V. Moulton, and P. J. Lockhart. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 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.
Key Words: consensus networks • genome-scale phylogeny • gene trees
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