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During the last decade, molecular techniques have contributed significantly to understanding sponge phylogeny. However, conflicting data have not resolved early metazoan evolution, and the interclass relationships of the Porifera are still debated. Complementary to the classical morphological and molecular biological approaches, the biomarker concept focusses on the occurrence and distribution of specific organic molecules, commonly lipids. These lipids reveal information on the biological source (sponge, associated microbes) and the biosynthetic and metabolic pathways involved in the formation of the respective compounds. Demosponges, best studied among the Porifera, are known to possess unusual membrane lipids, such as exotic sterols and the so-called demospongic fatty acids. These compounds are indicative for specific enzyme systems controlling biosynthetic properties like carbon chain elongation and the introduction of characteristic double bonds. Thus, they provide excellent targets for chemotaxonomic analyses at the class level. Our comprehensive biomarker study demonstrates that the Hexactinellida and the Demosponges share an ancestral design of lipid biosynthesis. That strategy involves the processing of bacterial precursor lipids and results in different biomembrane structures than found in contemporary organisms other than sponges. To the exclusion of the Calcarea, their unique lipid characteristics put the Hexactinellida and the Demospongiae into the same phylogenetic group. Moreover, biomarkers indicate similar patterns of Archaea and specific Eubacteria associated with the Hexactinellida and the Demospongiae.

Molecular markers have transformed our understanding of processes acting at the population level in marine invertebrates, including sponges. Due to the high level of morphological conservativeness over wide geographic distances, panmixia of sponge populations was assumed. However, allozyme studies of over 60 sponge species demonstrated that morphologically very similar allopatric populations almost invariably belonged to different species. Hence, cosmopolitanism in sponges is likely to be very rare, which has resulted in a profound change in modern sponge taxonomy. The application of DNA markers allowed for a shift towards more genealogical approaches, but mtDNA, most commonly used in other taxa, seems to be too conserved in sponges to be useful at the population level. CO1 sequences in populations of the demosponge Astrosclera willeyana, for example, are nearly invariant between Red Sea and Central Pacific. Up to now, most population-level analyses in sponges have concentrated on the rDNA internal transcribed spacers (ITS), which seem to provide good resolution at larger spatial scales. For example, analyses of ITS sequences have allowed inferences about historical and ecological factors shaping present day distributions of the Indo-Pacific coral reef calcareous sponge Leucetta chagosensis. However, because of the risk of paralogy, levels of intragenomic variation in the ITS multi-copy array must be investigated before it can be routinely used in phylogeographic studies. Additional markers such as microsatellites or single-copy nDNA markers (e.g. Introns) are only beginning to emerge. The application of such markers may provide data of higher resolution to improve our understanding of sponge genetics and phylogeography.

Reconstructing the phylogeny of sponges (Porifera) is one of the remaining challenges to resolve the metazoan Tree of Life and is a prerequisite for understanding early animal evolution. Molecular phylogenetic analyses for two of the three extant classes of the phylum, Demospongiae and Calcarea, are largely incongruent with traditional classifications, most likely because of a paucity of informative morphological characters and high levels of homoplasy. For the third class, Hexactinellida (glass sponges)--predominantly deep-sea inhabitants with unusual morphology and biology--we present the first molecular phylogeny, along with a cladistic analysis of morphological characters. We collected 18S, 28S, and mitochondrial 16S ribosomal DNA sequences of 34 glass sponge species from 27 genera, 9 families, and 3 orders and conducted partitioned Bayesian analyses using RNA secondary structure-specific substitution models (paired-sites models) for stem regions. Bayes factor comparisons of different paired-sites models against each other and conventional (independent-sites) models revealed a significantly better fit of the former but, contrary to previous predictions, the least parameter-rich of the tested paired-sites models provided the best fit to our data. In contrast to Demospongiae and Calcarea, our rDNA phylogeny agrees well with the traditional classification and a previously proposed phylogenetic system, which we ascribe to a more informative morphology in Hexactinellida. We find high support for a close relationship of glass sponges and Demospongiae sensu stricto, though the latter may be paraphyletic with respect to Hexactinellida. Homoscleromorpha appears to be the sister group of Calcarea. Contrary to most previous findings from rDNA, we recover Porifera as monophyletic, although support for this clade is low under paired-sites models.