Phylogenetic trees based on gene content.

Daniel H Huson; Mike Steel

doi:10.1093/bioinformatics/bth198

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Phylogenetic trees based on gene content.

Daniel H Huson·Mike Steel

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Abstract

UNLABELLED: 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 reconstruction 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 simplify 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. AVAILABILITY: http://www.ab.informatik.uni-tuebingen.de/software/genecontent/welcome_en.html

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Algorithms Chromosome Mapping Computer Simulation Evolution, Molecular Genetic Variation Likelihood Functions Models, Genetic Models, Statistical Phylogeny Sequence Alignment Sequence Analysis, DNA Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't Validation Study

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Daniel H Huson, Mike Steel. 2004-03-25. Phylogenetic trees based on gene content.. https://doi.org/10.1093/bioinformatics%2Fbth198

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