Ralf Aurahs

Publications of Ralf Aurahs

• A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA.

  Authors: Markus Göker, Guido W Grimm, Alexander F Auch, Ralf Aurahs, Michal Kučera

  Evolutionary bioinformatics online. 01/2010; 6:97-112.

  Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary toIdentifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices. Also, distance calculation is difficult for highly alignment-ambiguous sequences. Here, we applied a recently described clustering optimization method to highly divergent planktonic foraminifera SSU rDNA sequences. We determined the distance function and the clustering setting that result in the highest agreement with morphological reference data. Alignment-free distance calculation, when adapted to the use with partly non-homologous sequences caused by distinct primer pairs, outperformed multiple sequence alignment. Clustering optimization offers new perspectives for the barcoding of species diversity and for environmental sequencing. It bridges the gap between traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both genetic divergence and given species concepts.

• Geographical distribution of cryptic genetic types in the planktonic foraminifer Globigerinoides ruber.

  Authors: Ralf Aurahs, Guido W Grimm, Vera Hemleben, Christoph Hemleben, Michal Kucera

  Molecular ecology. 04/2009;

  Abstract We present SSU rDNA data resolving the seasonal and geographical distribution of 'cryptic' genetic types of the planktonic foraminifer morphospecies Globigerinoides ruber in the easternAbstract We present SSU rDNA data resolving the seasonal and geographical distribution of 'cryptic' genetic types of the planktonic foraminifer morphospecies Globigerinoides ruber in the eastern Atlantic Ocean and the Mediterranean Sea. Analysis of 262 sequences revealed the presence of five genetic types belonging to two distinct lineages. Although the morphospecies G. ruber occurs throughout the investigated region, its constituent 'cryptic' genetic types show a pattern of widespread exclusion, which is difficult to reconcile with the concept of ubiquitous dispersal. One of the newly discovered genetic types was exclusively found at stations in the Mediterranean Sea, possibly representing the smallest-scale example of endemism known in planktonic foraminifera. In general, our results suggest that the geographical scale of mutual exclusion between the genotypes is negatively correlated with their phylogenetic relatedness: the most similar and most recently diverged pair of siblings showed the strongest evidence for small-scale competitive exclusion. This pattern is consistent with the concept of niche partitioning, implying decreasing level of competition between genetic types with increasing degree of genetic divergence.

• Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences.

  Authors: Ralf Aurahs, Markus Göker, Guido W Grimm, Vera Hemleben, Christoph Hemleben, Ralf Schiebel, Michal Kucera

  Bioinformatics and biology insights. 01/2009; 3:155-77.

  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-basedThe 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.

• A revised taxonomic and phylogenetic concept for the planktonic foraminifer species Globigerinoides ruber based on molecular and morphometric evidence

  Authors: Ralf Aurahs, Yvonne Treis, Kate Darling, Michal Kucera

  Marine Micropaleontology.

  Recent SSU rDNA sequence data of the paleoceanographically important planktonic foraminifer species Globigerinoides ruber showed the presence of two distinct phylogenetic lineages within thisRecent SSU rDNA sequence data of the paleoceanographically important planktonic foraminifer species Globigerinoides ruber showed the presence of two distinct phylogenetic lineages within this morphotaxon. The first lineage (G. ruber sensu stricto) includes the genetic type that corresponds to pink-pigmented G. ruber, as well as three of the five genetic types recognised in individuals of “white” G. ruber (labelled Type Ia, Type Ib and Type Ib2). The remaining two genetic types of G. ruber (white), labelled as Types IIa and IIb, represent a distinct phylogenetic lineage (G. ruber sensu lato), closer related to Globigerinoides conglobatus. Here we combine molecular clock and morphometric analyses to shed light on the taxonomical and phylogenetic significance of the presence of these two distinct lineages within the morphotaxon G. ruber. A molecular clock approach suggests a rather recent origin of the G. ruber sensu stricto lineage in the late Miocene and a split between G. ruber (pink) and the “white” genotypes Ia, Ib and Ib2 around 6 Ma. This indicates that all records of G. ruber prior to the G. ruber “pseudo-extinction” event at 8 Ma refer to an unrelated species (Globigerinoides subquadratus) and that the G. ruber (pink) lineage is substantially older than the first appearance of the pink pigmentation in the fossil record. In order to establish the taxonomic identity of the G. ruber sensu lato phylogenetic lineage, we conducted morphometric measurements on (i) pictures of specimens with known genetic identity, (ii) shells from sediment samples, (iii) specimens assigned to G. ruber and Globigerinoides elongatus from a museum collection and (iv) pictures of G. ruber sensu lato morphotype from recent literature. Our results suggest that specimens of Type IIa that represent the G. ruber sensu lato lineage are morphologically identical to the concept of the G. ruber sensu lato morphotype in recent literature, and that these morphotypes are consistent with the species definition of Globigerinoides elongatus. We therefore propose that the name G. elongatus (sensu d'Orbigny) should be reinstated and used for the genetic Type IIa. The name G. ruber (sensu d'Orbigny) should be reserved for specimens of the pink chromotype. Specimens of Types Ia, Ib and Ib2 require new species names, but our data are not sufficient to provide a morphological character separating these species from their sister G. ruber (pink), other than by their shell colouration.