MBE Advance Access published online on May 12, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp102
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Research Article |
A phylogenetic mixture model for gene family loss in parasitic bacteria
School of Biological Sciences, University of Liverpool, UK
Correspondence: Matthew Spencer, School of Biological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK. Phone +44 (0)151 795 4399. Fax +44 (0)151 795 4404. Email m.spencer{at}liverpool.ac.uk
Received for publication March 4, 2009. Revision received April 27, 2009. Accepted for publication May 5, 2009.
Gene families are frequently gained and lost from prokaryotic genomes. It is widely believed that the rate of loss was accelerated for some but not all gene families in lineages that became parasites or endosymbionts. This leads to a form of heterotachy which may be responsible for the poor performance of phylogeny estimation based on gene content. We describe a mixture model which accounts for this heterotachy. We show that this model fits data on the distribution of gene families across bacteria from the COG database much better than previous models. However, it still favours an artefactual tree topology in which parasites form a clade over the more plausible 16S topology. In contrast to a previous model of genome dynamics, our model suggests that the ancestral bacterium had a small genome. We suggest that models of gene family gain and loss are likely to be more useful for understanding genome dynamics than for estimating phylogenetic trees.
Key Words: gene families • mixture model • parasites • maximum likelihood • phylogenetics