Comparative mitochondrial genomics in basal metazoans : new phylogenetic and functional approaches The phylum Placozoa is crucial for understanding the early evolutionary pathways of animal mitochondrial genomes. The studies conducted in this thesis target early metazoan mitochondrial phylogenetics placozoan mitochondrial mRNA processing and comparative placozoan mitochondrial genomics and its implications for placozoan taxonomy. In order to test the effect of taxon sampling on metazoan mitochondrial phylogenies five comprehensive whole mitochondrial data sets were generated and analyzed. The outcomes of the analyses support some well known topologies but also reveal some problematic taxa. In sum with respect to phylogenetics mitochondrial data sets perform best below the phylum level as current evolutionary models struggle with data heterogeneity and long branch attraction artifacts. Deep RNA sequencing revealed the existence of a single base pair cox1 micro exon but does not support mRNA editing in Placozoa. This cox1 micro exon is the first mitochondrial single base pair exon reported from an animal. The comparative analyses of nine new placozoan mitochondrial genomes revealed an unexpected diversity and complex evolutionary history of mitochondrial DNA characteristics within Placozoa. Complemented by nuclear genome data this mtDNA diversity yielded the formal description of the new placozoan genus Polyplacotoma. The analyses also provided new important insights into enrichment patterns of GC rich hairpins the evolution of gene orders and complex fragmentation patterns of placozoan mitochondrial genes.