@ARTICLE{TreeBASE2Ref15376, author = {Dirk Erpenbeck and Scott A. Nichols and Oliver Voigt and Martin Dohrmann and John N. A. Hooper and G. W?rheide}, title = {Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches - case studies with sponge LSU}, year = {2007}, keywords = {}, doi = {}, url = {}, pmid = {}, journal = {Journal of Molecular Evolution}, volume = {}, number = {}, pages = {}, abstract = {Many demosponge rDNA phylogenies result in trees, which are incongruent to either alternative gene tree reconstructions or morphological expectations. One reason for this outcome might be a suboptimal application of phylogenetic substitution models. While standard models describe the evolution of independently evolving characters fairly well, they are not suitable for sites coding for non-independent characters such as rRNA strands that form a helix in the ribosome. Such non-independent sites require the use of models, which take the co-evolution of the complete nucleotide pair (=doublet) into account. We analyzed 28SrDNA (LSU) demosponge phylogenies using such doublet models for pairing sites (rRNA-helices) and compared our findings with the results of standard approaches. We demonstrate that paired and unpaired sites of the same gene harbour different phylogenetic signals and that usage of doublet models results in significantly better demosponge trees. We show the influence of more sophisticated models on basal metazoan phylogeny and the phylogenetic relationships of demosponge orders.} }

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