Guido W Grimm

Publications of Guido W Grimm

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

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

  Evolutionary Bioinformatics. 01/2010;

• 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.

• Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling.

  Authors: Alexandros Stamatakis, Markus Göker, Guido W Grimm

  Evolutionary bioinformatics online. 01/2010; 6:73-90.

  The constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number ofThe constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number of base pairs, phylogenomic alignments) as well as vertical (number of taxa) dimension. Put aside the ongoing controversial discussion about appropriate models, partitioning schemes, and assembly methods for phylogenomic alignments, coupled with the high computational cost to infer these, for many organismic groups, a sufficient number of taxa is often exclusively available from one or just a few genes (e.g., rbcL, matK, rDNA). In this paper we address scalability of Maximum-Likelihood-based phylogeny reconstruction with respect to the number of taxa by example of several large nested single-gene rbcL alignments comprising 400 up to 3,491 taxa. In order to test the effect of taxon sampling, we employ an appropriately adapted taxon jackknifing approach. In contrast to standard jackknifing, this taxon subsampling procedure is not conducted entirely at random, but based on drawing subsamples from empirical taxon-groups which can either be user-defined or determined by using taxonomic information from databases. Our results indicate that, despite an unfavorable number of sequences to number of base pairs ratio, i.e., many relatively short sequences, Maximum Likelihood tree searches and bootstrap analyses scale well on single-gene rbcL alignments with a dense taxon sampling up to several thousand sequences. Moreover, the newly implemented taxon subsampling procedure can be beneficial for inferring higher level relationships and interpreting bootstrap support from comprehensive analysis.

• 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.

• Rooting and dating maples (Acer) with an uncorrelated-rates molecular clock: implications for north American/Asian disjunctions.

  Authors: Susanne S Renner, Guido W Grimm, Gerald M Schneeweiss, Tod F Stuessy, Robert E Ricklefs

  Systematic biology. 11/2008; 57(5):795-808.

  Simulations suggest that molecular clock analyses can correctly identify the root of a tree even when the clock assumption is severely violated. Clock-based rooting of phylogenies may be particularlySimulations suggest that molecular clock analyses can correctly identify the root of a tree even when the clock assumption is severely violated. Clock-based rooting of phylogenies may be particularly useful when outgroup rooting is problematic. Here, we explore relaxed-clock rooting in the Acer/Dipteronia clade of Sapindaceae, which comprises genera of highly uneven species richness and problematic mutual monophyly. Using an approach that does not presuppose rate autocorrelation between ancestral and descendant branches and hence does not require a rooted a priori topology, we analyzed data from up to seven chloroplast loci for some 50 ingroup species. For comparison, we used midpoint and outgroup rooting and dating methods that rely on rooted input trees, namely penalized likelihood, a Bayesian autocorrelated-rates model, and a strict clock. The chloroplast sequences used here reject a single global substitution rate, and the assumption of autocorrelated rates was also rejected. The root was placed between Acer and Dipteronia by all three rooting methods, albeit with low statistical support. Analyses of Acer diversification with a lineage-through-time plot and different survival models, although sensitive to missing data, suggest a gradual decrease in the average diversification rate. The nine North American species of Acer diverged from their nearest relatives at widely different times: eastern American Acer diverged in the Oligocene and Late Miocene; western American species in the Late Eocene and Mid Miocene; and the Acer core clade, including A. saccharum, dates to the Miocene. Recent diversification in North America is strikingly rare compared to diversification in eastern Asia.

• Its evolution in Platanus (Platanaceae): homoeologues, pseudogenes and ancient hybridization.

  Authors: Guido W Grimm, Thomas Denk

  Annals of botany. 03/2008; 101(3):403-19.

  BACKGROUND AND AIMS: Platanaceae is an old family of angiosperms extending back to the Early Cretaceous but consisting of a single extant genus, Platanus. Species of Platanus have long been known toBACKGROUND AND AIMS: Platanaceae is an old family of angiosperms extending back to the Early Cretaceous but consisting of a single extant genus, Platanus. Species of Platanus have long been known to hybridize, and the London plane, Platanus x hispanica, is a well-known example of a hybrid species that formed in historical times. In addition, morphological studies have suggested past interspecific or interlineage hybridization and reticulation as possibly important factors in the evolution of the genus. This study aims at unravelling the complex evolutionary information contained in internal transcribed spacer (ITS) sequences. METHODS: The ITS of the 35S nuclear ribosomal DNA are biparentally inherited, multi-copy markers with a high potential for resolving intrageneric relationships especially when ancient hybridization (reticulation) is involved. Phylogenetic trees, splits graphs and motif analysis are used to extract phylogenetic information from 223 cloned ITS sequences, representing ten species and varieties of Platanus. Non-pseudogenous and pseudogenous sequence motives are assessed to explain how different evolutionary modes contribute to possibly conflicting character state patterns in the ITS. KEY RESULTS: It was found that putative non-functional ITS copies ('pseudogenes') form distinct groups in phylograms and splits graphs, and that pseudogenous lineages reflect ancient hybridization events conserved in the ITS. Specifically, pseudogenous clones of an 'Atlantic' North American clade share sequence motives with non-pseudogenous clones of the western ('Pacific') North American P. racemosa species aggregate. In addition, evidence was found for recent lateral gene flow as a possible factor in the evolution of the central Mexican P. rzedowskii. CONCLUSIONS: Broad ITS data sets that cover intra- and interindividual variability reveal past and ongoing speciation processes in Platanus. Evolutionary pathways can be visualized with splits graphs, but not with bifurcating trees.

• General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability.

  Authors: Markus Göker, Guido W Grimm

  BMC evolutionary biology. 02/2008; 8:86.

  BACKGROUND: Amongst the most commonly used molecular markers for plant phylogenetic studies are the nuclear ribosomal internal transcribed spacers (ITS). Intra-individual variability of theseBACKGROUND: Amongst the most commonly used molecular markers for plant phylogenetic studies are the nuclear ribosomal internal transcribed spacers (ITS). Intra-individual variability of these multicopy regions is a very common phenomenon in plants, the causes of which are debated in literature. Phylogenetic reconstruction under these conditions is inherently difficult. Our approach is to consider this problem as a special case of the general biological question of how to infer the characteristics of hosts (represented here by plant individuals) from features of their associates (represented by cloned sequences here). RESULTS: Six general transformation functions are introduced, covering the transformation of associate characters to discrete and continuous host characters, and the transformation of associate distances to host distances. A pure distance-based framework is established in which these transformation functions are applied to ITS sequences collected from the angiosperm genera Acer, Fagus and Zelkova. The formulae are also applied to allelic data of three different loci obtained from Rosa spp. The functions are validated by (1) phylogeny-independent measures of treelikeness; (2) correlation with independent host characters; (3) visualization using splits graphs and comparison with published data on the test organisms. The results agree well with these three measures and the datasets examined as well as with the theoretical predictions and previous results in the literature. High-quality distance matrices are obtained with four of the six transformation formulae. We demonstrate that one of them represents a generalization of the Sørensen coefficient, which is widely applied in ecology. CONCLUSION: Because of their generality, the transformation functions may be applied to a wide range of biological problems that are interpretable in terms of hosts and associates. Regarding cloned sequences, the formulae have a high potential to accurately reflect evolutionary relationships within angiosperm genera, and to identify hybrids and ancestral taxa. These results corroborate earlier ones which showed that treelikeness measures are a valuable tool in comparative studies of biological distance functions.

• A nuclear ribosomal DNA phylogeny of acer inferred with maximum likelihood, splits graphs, and motif analysis of 606 sequences.

  Authors: Guido W Grimm, Susanne S Renner, Alexandros Stamatakis, Vera Hemleben

  Evolutionary bioinformatics online. 02/2006; 2:7-22.

  The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) andThe multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong's (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.

• Patterns of molecular and morphological differentiation in Fagus (Fagaceae): phylogenetic implications.

  Authors: Thomas Denk, Guido W Grimm, Vera Hemleben

  American journal of botany. 06/2005; 92(6):1006-16.

  To study phylogenetic relationships among species of Fagus, the internal transcribed spacer regions ITS1 and ITS2 of the nuclear ribosomal DNA and morphological data were analyzed. Both molecular andTo study phylogenetic relationships among species of Fagus, the internal transcribed spacer regions ITS1 and ITS2 of the nuclear ribosomal DNA and morphological data were analyzed. Both molecular and morphologically based phylogenies suggest that Eurasian species of Fagus subgenus Fagus are basal to the North American Fagus grandifolia. The subgenus Fagus is a paraphyletic group basal to three East Asian species forming the subgenus Engleriana. Due to a considerably large amount of DNA polymorphism, relationships among basal species of Fagus could not be entirely resolved when analyzing ITS sequences with standard methods. Morphological trees helped to resolve more clearly relationships within the subgenus Fagus. The East Asian F. hayatae is suggested to be basal to the rest of the genus. This hypothesis is further supported by distinctive patterns of nucleotide variability found for ITS regions, allowing for basic and derived types to be distinguished. The high degree of ITS polymorphism within Fagus can be explained by (1) the complex evolutionary behavior of this marker, (2) the stenoecious ecological characteristic of Fagus with respect to its continuous geographic range throughout much of the Cenozoic, and (3) the absence of major radiations into further habitats as occurred in other Fagaceae.

• Diversity of rDNA in Chilostomella: Molecular differentiation patterns and putative hermit types

  Authors: Guido W. Grimm, Karin Stögerer, Kemal Topaç Ertan, Hiroshi Kitazato, Michal Kučera, Vera Hemleben, Christoph Hemleben

  Marine Micropaleontology.

  We present new data on nuclear DNA sequences coding for the 3′ region of the small subunit ribosomal RNA (SSU rDNA), the 5.8 subunit and the internal transcribed spacers (ITS1 and ITS2). 56 SSU rDNAWe present new data on nuclear DNA sequences coding for the 3′ region of the small subunit ribosomal RNA (SSU rDNA), the 5.8 subunit and the internal transcribed spacers (ITS1 and ITS2). 56 SSU rDNA and 23 ITS clones were obtained from 12 specimens of the genus Chilostomella collected in the Pacific Ocean, the Atlantic Ocean and the Mediterranean at depth between 600 and 1500 m. Surprisingly, the sequences could be attributed to a number of highly divergent SSU genotypes which cluster in different parts of the foraminiferal SSU rDNA phylogeny. One genetic type, found in most Chilostomella individuals, shows affinity to calcareous foraminifera and its phylogenetic position is consistent with the morphological classification of the genus. We call this genetic type “domestic”, to highlight the anomalous nature of the other obtained SSU rDNA types. The “domestic” sequences (SSU rDNA and ITS) indicate the presence of three distinct genetic types within Chilostomella of which one is limited to the Atlantic–Mediterranean and the other two were found in the Pacific Ocean, both co-occurring at one locality in the Sagami Bay. Albeit limited in size, our dataset provides the first indication for ocean-wide dispersal in bathyal benthic foraminifera. Five other foraminiferal SSU rDNA types were identified among the cloned sequences, all clustering outside the well-supported calcareous clade. The presence of these “contaminant” or “hermit” sequences indicates that calcareous tests of bathyal foraminifera may be inhabited or invaded by other non-calcareous taxa. This has implications for the recognition of standing stocks of individual benthic foraminiferal species in the deep-sea. Using cytoplasm staining techniques, these tests would be considered representative of a living individual of the species that produced the test.