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© 2005 Society of Systematic Biologists
Gene Family Content-Based Phylogeny of Prokaryotes: The Effect of Criteria for Inferring Homology
1 Department of Biological Sciences, University of South Carolina Columbia, South Carolina 29205, USA E-mail: austin{at}biol.sc.edu (A.L.H.)
2 Department of Computer Science and Engineering, University of South Carolina Columbia, South Carolina 29205, USA
Edited by Peter Lockhart: Associate Editor Chris Simon Editor
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Abstract |
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A number of recent papers have suggested that gene family content can be used to resolve phylogenies, particularly in the case of prokaryotes, in which extensive horizontal gene transfer means that individual gene phylogenies may not mirror the organismal phylogeny. However, no study has yet examined how sensitive such analyses are to the criterion of homology assessment used to assemble multigene families. Using data from 99 completely sequenced prokaryotic genomes, we examined the effect of homology criteria in phylogenetic analyses wherein presence or absence of each family in the genome was used as a cladistic character. Different criteria resulted in evidence for contradictory tree topologies, sometimes with high bootstrap support. A moderately strict criterion seemed best for assembling multigene families in a biologically meaningful way, but it was not necessarily preferable for phylogenetic analysis. Instead, a very strict criterion, which broke up gene families into smaller subfamilies, seemed to have advantages for phylogenetic purposes. The poor performance of gene family content-based phylogenetic analysis in the case of prokaryotes appears to reflect high levels of homoplasy resulting not only from horizontal gene transfer but also, more importantly, from extensive parallel loss of gene families in certain bacteria genomes.
Keywords: Gene content; gene families; gene loss; horizontal gene transfer; phylogenetic methods
Received December 22, 2003; Revised August 6, 2004; Accepted October 31, 2004
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