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Bioinformatics Advance Access published online on March 25, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth198
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received September 10, 2003
Revised December 19, 2003
Accepted January 14, 2004

Article

Phylogenetic trees based on gene content

Daniel H. Huson 1* Mike Steel 2

1 Center for Bioinformatics (ZBIT), Tübingen University, Sand 14, 72076 Tübingen, Germany
2 Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand

* To whom correspondence should be addressed. E-mail: huson{at}Informatik.uni-tuebingen.de.


  Abstract

Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper we derive a maximum likelihood estimation of evolutionary distance between species under a simple model of gene genesis and gene loss. Using simulated data on a biological tree with 107 taxa (and on a number of randomly generated trees) we compare the accuracy of tree re-construction using this ML distance measure to an earlier ad-hoc distance. We then compare these distance-based approaches to a character-based tree reconstruction method (Dollo parsimony) which seems well-suited to the analysis of gene content data. To simply simulations, we give a formal proof of the well known "fact" that the Dollo parsimony score is independent of the choice of root. Our results show a consistent trend, with the character-based method and ML distance measure outperforming the earlier ad-hoc distance method.


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