Grimm, Guido W.

Hemleben, Christoph

Hemleben, Vera

Sprenger, Dennis

English

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191Molecular evolution of the foraminiferal SSU rDNA:Prospects and pitfallsGuido W. Grimm1; Dennis Sprenger1; Christoph Hemleben1 & Vera Hemleben21Institute of Geosciences, University of Tübingen, Sigwartstrasse 10, 72076 Tübingen,Germany   guido.grimm@uni-tuebingen.de2Department of General Genetics, Centre of Plant Molecular Biology (ZMBP),University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, GermanyRibosomal DNA (rDNA) sequences have been extensively used forbenthic and pelagic foraminifera as a molecular marker to infer phylogenetichypotheses. However, molecular phylogenetic studies on a broad taxonomicset of foraminifera are characterized by a generally low resolution caused bythe low sequence divergence within the conserved sequence regions that canbe unambiguously aligned. Only a few moderately to well-supported lineages(e.g. miliolids, “polythalamous clade”, spinose planktonic taxa) have beenidentified; the phylogenetic backbone remains completely unresolved.Furthermore, the phylograms’ topologies and the inference of an “allforaminiferal root” appear to be heavily influenced by taxon sampling andoutgroup taxa that are used. Using phylogenetic networks, we can visualizethe extent and systematic bias induced by incompatible phylogenetic splits thatare predominant within the generally alignable portions of SSU (small subunit)rDNA data and thus hindered phylogenetic tree building up to now. We candemonstrate that SSU sequence data of foraminifers cannot be used ad hoc toinfer an “all-foraminiferal” phylogenetic hypothesis. However, the particulardata structure of the foraminiferal SSU showing an alteration between highlyconserved and highly divergent sequence portions provides a possibility toevaluate phylogenetic alternatives indicated by network analysis. Identificationof evolutionary hotspots for different taxonomic levels can reveal deep insightsin the pathways of molecular evolution of the foraminiferal SSU. Sequencemotives, e.g. in the DNA region coding for the terminal loop of helix 44, andalignability of variable regions are diagnostic for many taxonomic groups. Thus,an adequate pre-analyses filtering and organisation of the SSU rDNA data andtaxa analysed can help to produce a data set assessable for phylogenetic studies,which focuses on particular relationships and evolutionary hypotheses.Anuár io do Inst i tu to de Geociências -  UFRJISSN 0101-9759                        Vol. 29 - 1 / 2006  p. 191FORAMS  2006

Molecular evolution of the foraminiferal SSU rDNA: prospects and pitfalls

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Molecular evolution of the foraminiferal SSU rDNA: prospects and pitfalls

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