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Methods for Inference of Metazoan Phylogeny Using Mitochondrial Genome Arrangement DataGuido Fritzsch Interdisciplinary Centre for Bioinformatics Leipzig University Martin Schlegel Institute for Biology II Molecular Evolution & Animal Systematic Leipzig University Peter F. Stadler Bioinformatics Group Institute for Computer Science University of Leipzig Bernd Schierwarter Institute of Animal Ecology and Cell Biology, Ecology and Evolution Univ. of Veterinary Medicine Hannover Martin Middendorf, Matthias Bernt Faculty for Mathematics and Informatics University of Leipzig Mitochondrial genomes have been a particularly fruitful data set for phylogenetic reconstructions. Due to their limited size and the availability of a large number of informative data sets, they are particularly interesting for the reconstruction of deep metazoan phylogeny, i.e., the evolution of all animals except protozoans and sponges. Our research is based on two established methods for inferring phylogenies, namely multiple genome rearrangements as well as circular alignments. The latter approach is based on detecting blocks of genes whose order has been preserved during evolution. In a recent study, this approach has been pursued in detail within our group (1). The genome rearrangement approach, based on detecting rearrangements of blocks of genes rather than preserved order, has been examined by a collaborating work group at the University of Leipzig's department of computer science (2). 
A major part of our research is to develop new phylogenetic methods and refined models of evolution using these two methods as a starting point. In cooperation with the University of Leipzig's zoology group, a second major part of our research deals with processing newly acquired and analyzed mitochondrial genome sequences. Examining these data with our improved phylogenetic methods allows us to resolve open questions concerning the evolutionary roles and relationships between certain taxa such as Porifera, Placozoa, Cnidaria and Bilateria (including Hemichordata, Echinodermata and Chordata). Such insights finally contribute to the reconstruction of the so called Cambrian explosion, which is one of the prime challenges in metazoan evolution. 
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