Abstract
Unravelling the phylogenetic relationships of sponges (Phylum Porifera) is an important as well as challenging task. It helps the understanding of character evolution among early branching metazoans but also aids in bioprospecting for valuable bioactive sponge compounds. However, the phylogenetic relationships among Porifera are largely unsolved, because the simple poriferan bauplan frequently prevents unambiguous taxonomic species assignment and a clear definition of morphological synapomorphies is difficult (see e.g. Boury-Esnault 2006). DNA sequence markers are frequently employed to overcome morphological shortcomings in phylogeny (e.g. Kelly Borges et al. 1991) and taxonomy (e.g. DNA barcoding, see Wörheide & Erpenbeck 2007). However, some DNA markers suffer from insufficient phylogenetic signal (see e.g. Duran et al. 2004 and Wörheide 2006 on CO1 in population studies) and unequal evolutionary rates among taxa (see e.g. Erpenbeck et al. 2004 on 28S in Haplosclerida). Therefore, a careful evaluation and selection of molecular markers for each individual project is required.
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