Molecular evolution of some selected benthic foraminifera as inferred from sequences of the small subunit ribosomal DNA

Up to now the benthic foraminiferal classification is based mainly on morphological characters leading to controversies and systematic rearrangements. Previous molecular phylogenetic studies using nuclear encoded small subunit (SSU) rDNA as a marker were able to resolve some of the major divergence points. However, they partly contradicted the morphological findings and had difficulties to resolve convincingly the phylogenetic relationships, especially within the multilocular agglutinated and calcitic orders. To further enlarge our knowledge about these phylogenetic relationships, we collected specimens of deep-sea benthic taxa from the Atlantic, the Pacific, the Mediterranean, and the Sea of Marmara, and classified single individuals by a combination of morphological methods (scanning electron microscope (SEM) and light microscope) and molecular tools (sequencing of SSU rDNA). In addition, we developed RNA secondary structure models of the sequenced part of the SSU rDNA, which allowed to determine exactly homologous nucleotide positions and to optimize the alignments used for the phylogenetic analyses. To illustrate the improvement of the methodology, the analyses were carried out together with sequences used in several former studies. The analysis was performed in several steps to find always suitable outgroups for the consecutively following tree construction, starting with the conserved regions for the basal phylogeny and including an increasing amount of variable but alignable regions to improve the resolution of phylogenetically younger groups. Within the limited number of sequenced taxa, the results presented here are, in general, consistent with the fossil record and existing morphological classification. The astrorhizids (agglutinated tests) with the oldest fossil record form the most ancient foraminiferal group. The selected allogromid taxa with organic tests appear to have evolved parallel to a cluster comprising lituolids (agglutinated tests), the porcelaneous miliolids (high magnesium calcite), and multilocular agglutinated and calcitic foraminifers. Furthermore, the calcitic taxa (e.g., buliminids and rotaliids) and the genera Trochammina and Textularia with agglutinated tests appear to be descendants of the stratigraphically older agglutinated foraminifers. Differences to the morphological classification are mainly found at family and genus level within the calcitic foraminifera.