Sponges are simple animals that mostly inhabit the marine ecosystem. The role of sponges in the marine ecosystem and the potential of their bioactive compounds for the pharmaceutical industry have already been reviewed. Because of the extensive investigations of sponges within those two disciplines, marine ecology and chemistry, sponges are among the best-studied Metazoa. Likewise, sponges have been selected as animal models for investigating the origin of the multicellularity because sponges have a simple body structure and physiology (e.g., lack of nervous and circulatory organs). Due to their diversity and abundance in the tropics, particularly in the Indo-Pacific, sponges have also attracted taxonomists, systematists and ecologists to assess their diverseness and their phylogenetic and phylogeographic relationships. Resolving those research questions is difficult, because sponges are categorised as comparatively character poor taxa. By using only conservative taxonomy or systematics, the sponge diversity might therefore be underestimated. Inevitably, sponge biologists have to employ molecular methods as additional tools.

In this research, molecular tools were used in order to analyse the taxonomy, phylogeny and phylogeographic relationships of selected sponge species. Xestospongia testudinaria & Neopetrosia exigua (Family Petrosiidae, Order Haplosclerida) were selected because of their conspicuousness in the Indo-Pacific coral reef ecosystems, whereby Xestospongia testudinaria is prominently known as the Indo-Pacific giant barrel sponge. Additionally, the order Haplosclerida has been described as an example of sponge order that has been examined systematically for a number of years and displays major discrepancy between morphology and molecular phylogenies. Molecular data suggests that the order needs revision at all taxonomic levels, which is the cause for further conflicts between taxonomists and systematists. In my research I focused mostly on sponge samples that originated from South East Asia or the Indo-Australian Archipelago (IAA). This region represents one of the best-explored marine regions in the Indo-Pacific. The aim of my research is to discover to what extent molecular tools are suitable to detect a phylogenetic signal, a phylogeographical break or a genotypic difference in the two selected sponge taxa.

Several markers from the mitochondrial (mtDNA), ribosomal (rRNA) and nuclear (nucDNA) have been utilised. The 3' partition of the cytochrome oxidase subunit 1 (I3-M11 of cox1) from the mtDNA could be used to detect a genetic structure in Xestospongia testudinaria in a geographical narrow scale study of < 200 km2 in Lembeh, North Sulawesi, Indonesia (Chapter 6) and throughout the Indo-Pacific despite limitations in the sample datasets (Chapter 2). In addition, the presence of a species complex in X. testudinaria was detected with the aid of phylogenetic reconstructions from a concatenation of mtDNA sequences (I3-M11 of cox1 and the Adenosine Triphosphate Synthase F0 subunit 6 / ATP6), and a nucDNA marker, the Adenosine Triphosphate Synthase β subunit intron (ATPS-β intron) (Chapter 6). At the same time, the presence of a species complex in X. testudinaria was recognised in a broader scale study of the Indo-Australian Archipleago (IAA) (Chapter 3). As a result, selected mtDNA and nucDNA markers in this thesis are useful for the investigation of the taxonomical status and phylogeographical relationships of X. testudinaria. A phylogeographical break in the IAA region due to the Pleistocene low sea level and Holocene recolonisation events (Chapter 3) could not be recovered among X. testudinaria in a phylogeographical analysis. Similarly, overlapping I3-M11 cox1 haplotypes between X. testudinaria, X. muta and X. bergquistia were recovered. This might be due to the presence of ancient polymorphisms on the barrel sponge mtDNA markers.

Molecular tools are also used to help identifying my second selected sponge s