Molecular phylogeny of Eubacteria: a new multiple tree analysis method applied to 15 sequence data sets questions the...

Phylogenetic relationships between the major eubacterial phyla were studied using the sequences of 15 homologous bacterial genes. Neither the classical concatenation strategy nor a new multiple tree analysis method involving statistical tests of the inferred phylogenetic relationships provided any (solid) conclusions about eubacterial phylogeny; no pairs of eubacterial phyla proved to be closer to each other in the 15 reconstructed trees than would be expected for trees with random topologies. The phylogeny of Eubacteria therefore appears to be tightly bush-like. Moreover, results from both concatenation and multiple tree analysis raise doubts concerning the monophyly of the so-called Gram-positive bacteria phylum, since the monophyly hypothesis is no more strongly supported by data than its alternatives. It is noteworthy that the structural bases for the Gram-positive phenotype are not incompatible with the hypothesis of independent emergence of this character at two different times.