Project Info

RNA-Based Deep Metazoan Phylogeny

Non-coding RNA molecules, in particular ribosomal RNAs, are a major data source in molecular phylogenetics. Only very recently, however, the peculiarities of RNA evolution, and in particular the long-time conservation of their secondary structures, have been taken into account in this context. We therefore propose: (1) A re-evaluation of the existing rRNA data using a Bayesian approach that explicitly takes into account conserved functional secondary structure elements. (2) The development of algorithms and a convenient software implementation for deriving reliable secondary structure models of novel rRNA sequences (both 18S and 28S) that will be sequenced in the context of the SPP Deep Metazoan Phylogeny SPP. (3) A systematic investigation of the phylogenetic information content of other noncoding RNA classes, with a focus on data that will be contained in the EST surveys performed by many of the participating research groups in the Metazoan Deep Phylogeny. (4) The development of methods for utilizing the evolution of the secondary structures themselves for reconstructing phylogenies. (5) The development of nucleotide substitution models that not only distinguish between conserved helices and \other" regions in a sample of non-coding RNAs, but also incorporate the slower evolution of the structural elements itself. As part of the proposed research project we will eventually provide improved software for rRNA based phylogeny to the research community. The efforts outlined above will profit directly from data produced by participating research groups: the reliability of structural models for rRNAs for poorly covered taxonomic groups can be assessed as soon as an increasing amount of data becomes available. On the other hand, preliminary versions of our software will be made accessible to participating research groups so that new sequences can be analyzed in a timely fashion.

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Prof. Dr. Peter F. Stadler, Universitaet Leipzig, Leipzig