Ralf Aurahs¹, Markus Göker^2,3, Guido W. Grimm⁴, Vera Hemleben⁵, Christoph Hemleben¹, Ralf Schiebel⁶ and Michal Kučera<sup>1

1</sup>Department of Micropaleontology, Institute of Geosciences, Eberhard Karls University of Tübingen, Sigwartstrabe 10, 72076 Tübingen, Germany. ²Organismic Botany, Eberhard Karls University of Tübingen, Auf der Morgenstelle 1, 72076 Tübingen, Germany. ³DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstrabe 7 B, 38124 Braunschweig, Germany. ⁴Department of Palaeobotany, Natural History Museum, Box 50007, 10405 Stockholm, Sweden. ⁵Department of General Genetics, Centre of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany. ⁶Laboratoire des Bio-Indicateurs Actuels et Fossiles, University of Angers, 2 bd Lavoisier, 49045 Angers, France.

Abstract

The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences. Our multiple analysis approach is based on eleven different automated alignments, analysed separately under the maximum likelihood criterion. The high degree of congruence between the phylogenies derived from our novel approach, traditional manually homologized culled alignments and the fossil record indicates that poorly resolved nucleotide homology does not represent the most significant obstacle when exploring the phylogenetic structure of the SSU rDNA in planktonic foraminifera. We show that approaches designed to extract phylogenetically valuable signals from complete sequences show more promise to resolve the backbone of the planktonic foraminifer tree than attempts to establish strictly homologous base calls in a manual alignment.