Mitogenomics at the base of Metazoa

•A broad mitochondrial genome diversity exists at the base of Metazoa.•Phylogenetic relationships among basal metazoans are unresolved.•We analyzed large mitochondrial data sets to illuminate basal metazoan relationships.•The fast evolving Ctenophora and Hexactinellida are sensitive to analyses artifacts.•Available mt data is currently only suitable for lower level inferences.

Unraveling the base of metazoan evolution is of crucial importance for rooting the metazoan Tree of Life. This subject has attracted substantial attention for more than a century and recently fueled a burst of modern phylogenetic studies. Conflicting scenarios from different studies and incongruent results from nuclear versus mitochondrial markers challenge current molecular phylogenetic approaches. Here we analyze the presently most comprehensive data sets of mitochondrial genomes from non-bilaterian animals to illuminate the phylogenetic relationships among early branching metazoan phyla. The results of our analyses illustrate the value of mitogenomics and support previously known topologies between animal phyla but also identify several problematic taxa, which are sensitive to long branch artifacts or missing data.

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