MBE Advance Access originally published online on February 22, 2006
Molecular Biology and Evolution 2006 23(5):1019-1030; doi:10.1093/molbev/msj113
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Research Article |
Visualizing and Assessing Phylogenetic Congruence of Core Gene Sets: A Case Study of the 
-Proteobacteria
* Genome Atlantic, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada; and Canadian Institute for Advanced Research and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
E-mail: eric.bapteste{at}dal.ca.
Here, we address a much-debated topic: is there or is there not an organismal tree of 
-proteobacteria that can be unambiguously inferred from a core of shared genes? We apply several recently developed analytical methods to this problem, for the first time. Our heat map analyses of P values and of bootstrap bipartitions show the presence of conflicting phylogenetic signals among these core genes. Our synthesis reconstruction suggests that at least 10% of these genes have been laterally transferred during the divergence of the -proteobacteria, and that for most of the rest, there is too little phylogenetic signal to permit firm conclusions about the mode of inheritance. Although there is clearly a central tendency in this data set (it is far from random), lateral gene transfers cannot be ruled out. Instead of an organismal tree, we propose that these core genes could be used to define a more subtle and partially reticulated pattern of relationships.
Key Words: -proteobacteria • phylogeny • heat map • congruence
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