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Phylogenetic Analyses Under Secondary Structure-Specific Substitution Models Outperform Traditional Approaches: Case Studies with Diploblast LSU

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Abstract

Many rDNA molecular phylogenetic studies result in trees that are incongruent to either alternative gene tree reconstructions and/or morphological assumptions. One reason for this outcome might be the application of suboptimal phylogenetic substitution models. While the most commonly implemented models describe the evolution of independently evolving characters fairly well, they do not account for character dependencies such as rRNA strands that form a helix in the ribosome. Such nonindependent sites require the use of models that take into account the coevolution of the complete nucleotide pair (doublet). We analyzed 28S rDNA (LSU) demosponge phylogenies using a “doublet” model for pairing sites (rRNA-helices) and compared our findings with the results of “standard” approaches using Bayes factors. We demonstrate that paired and unpaired sites of the same gene result in different reconstructions and that usage of a doublet model leads to more reliable demosponge trees. We show the influence of more sophisticated models on phylogenetic reconstructions of early-branching metazoans and the phylogenetic relationships of demosponge orders.

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Acknowledgments

The authors thank the supercomputing facility of the University of Göttingen and Johan Nylander for advice on Bayes factors. Jeff Thorne and another, anonymous reviewer provided excellent suggestions to improve the manuscript. D.E. acknowledges financial support from the European Union under a Marie-Curie outgoing fellowship (MOIF-CT-2004 Contract No. 2882). G.W. acknowledges financial support from the German Research Foundation (DFG; Projects Wo896/3, 5), through the DFG Priority Program SPP1174 “Deep Metazoan Phylogeny” (Project Wo896/6), and the European Marie-Curie project HOTSPOTS (Contract MEST-CT-2005-020561).

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Correspondence to Dirk Erpenbeck.

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Erpenbeck, D., Nichols, S.A., Voigt, O. et al. Phylogenetic Analyses Under Secondary Structure-Specific Substitution Models Outperform Traditional Approaches: Case Studies with Diploblast LSU. J Mol Evol 64, 543–557 (2007). https://doi.org/10.1007/s00239-006-0146-3

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