Dr. Matthias Wolf Lecturer (Akademischer Rat, AR) Department of Bioinformatics Biocenter (Theodor-Boveri-Institute) Bayerische Julius-Maximilians University of Würzburg Am Hubland, D-97074 Würzburg, Germany
Short Curriculum Nov 2008-today Lecturer (tenured faculty position), Department of Bioinformatics, University of Würzburg, Germany Jan 2003-Oct 2008 Assistant Professor, Department of Bioinformatics, University of Würzburg, Germany Oct 2002-Dec 2002 Visiting Scientist (Postdoc), Research Centre Juelich, Germany Oct 1999-Sep 2002 PhD studies, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin Research Association, Department of Limnology of Stratified Lakes, Stechlin-Neuglobsow, Germany Dec 1997-Jan 1998 Research Assistant, Senckenbergischen Naturforschenden Gesellschaft Frankfurt, Germany Apr 1993-Sep 1999 Undergraduate/Graduate studies in Biology, Free University of Berlin, Germany
Service as Reviewer Syst Biol, Mol Phylogenet Evol, Nucleic Acids Res, PLoS ONE, BMC Evol Biol, Bioinformatics, Planta, J Mol Evol, Plant Syst Evol, Mol Ecol, J Phycol, Phycologia, Gene, BMC Genomics, BMC Bioinformatics, J Eukaryot Microbiol, Protist, Conserv Genet, Biologia, BioTechniques, J Zool Syst Evol Res, Acta Tropica, Diatom Res, Nova Hedwigia, NSF - National Science Foundation, ISBRA - International Symposium on Bioinformatics Research and Applications, GIF - German-Israeli Foundation for Scientific Research and Development
h-index (60 publications in total) 19 (ISI Web of Knowledge); 20 (Scopus, google scholar)
Grants 2007-2010 DFG (German Research Foundation) grant MU 2831/1-1 (Co-PI) "Species phylogeny and the 'tree of life' based on an ITS2 sequence-structure Database and new algorithms"
Software The ITS2 Database, ProfDist, ProfDistS, 4SALE, CBCAnalyzer, A Java Applet for Exploring the New Higher Level Classification of Eukaryotes
Abstract: Background and Aims The green algal class Chlorophyceae comprises five orders (Chlamydomonadales, Sphaeropleales, Chaetophorales, Chaetopeltidales and Oedogoniales). Attempts to resolve the relationships among these groups have met with limited success. Studies of single genes (18S rRNA, 26S rRNA, rbcL or atpB) have largely failed to unambiguously resolve the relative positions of Oedogoniales, Chaetophorales and Chaetopeltidales (the OCC taxa). In contrast, recent genomics analyses of plastid data from OCC exemplars provided a robust phylogenetic analysis that supports a monophyletic OCC alliance. Methods An ITS2 data set was assembled to independently test the OCC hypothesis and to evaluate the performance of these data in assessing green algal phylogeny at the ordinal or class level. Sequence-structure analysis designed for use with ITS2 data was employed for phylogenetic reconstruction. Key Results Results of this study yielded trees that were, in general, topologically congruent with the results from the genomic analyses, including support for the monophyly of the OCC alliance. Conclusions Not all nodes from the ITS2 analyses exhibited robust support, but our investigation demonstrates that sequence-structure analyses of ITS2 provide a taxon-rich means of testing phylogenetic hypotheses at high taxonomic levels. Thus, the ITS2 data, in the context of sequence-structure analysis, provide an economical supplement or alternative to the single-marker approaches used in green algal phylogeny.
Abstract: The internal transcribed spacer 2 (ITS2) has been used as a phylogenetic marker for more than two decades. As ITS2 research mainly focused on the very variable ITS2 sequence, it confined this marker to low-level phylogenetics only. However, the combination of the ITS2 sequence and its highly conserved secondary structure improves the phylogenetic resolution(1) and allows phylogenetic inference at multiple taxonomic ranks, including species delimitation(2-8). The ITS2 Database(9) presents an exhaustive dataset of internal transcribed spacer 2 sequences from NCBI GenBank(11) accurately reannotated(10). Following an annotation by profile Hidden Markov Models (HMMs), the secondary structure of each sequence is predicted. First, it is tested whether a minimum energy based fold(12) (direct fold) results in a correct, four helix conformation. If this is not the case, the structure is predicted by homology modeling(13). In homology modeling, an already known secondary structure is transferred to another ITS2 sequence, whose secondary structure was not able to fold correctly in a direct fold. The ITS2 Database is not only a database for storage and retrieval of ITS2 sequence-structures. It also provides several tools to process your own ITS2 sequences, including annotation, structural prediction, motif detection and BLAST(14) search on the combined sequence-structure information. Moreover, it integrates trimmed versions of 4SALE(15,16) and ProfDistS(17) for multiple sequence-structure alignment calculation and Neighbor Joining(18) tree reconstruction. Together they form a coherent analysis pipeline from an initial set of sequences to a phylogeny based on sequence and secondary structure. In a nutshell, this workbench simplifies first phylogenetic analyses to only a few mouse-clicks, while additionally providing tools and data for comprehensive large-scale analyses.
Abstract: Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.
Abstract: In this study five different molecular markers were used to: (1) infer the phylogeographic differentiation of Thalassiosira weissflogii in the Atlantic and Pacific Oceans; and (2) address the biological species status of the inferred geographic lineages. The results of the ribosomal RNA data analyses suggested that the Hawaiian isolate evolved first after which the Indonesian and the Atlantic/California strains diverged. In contrast, the tree derived from the partial sexually induced gene 1 (Sig1) data exhibited an initial divergence between the Eastern Atlantic/Western Atlantic/California and the Hawaiian/Indonesian groups after which the latter evolved into the Hawaiian and Indonesian lineages. The partial beta-tubulin phylogeny discerns an early "split" between an Eastern Atlantic/Western Atlantic clade and an Indonesia/California/Hawaii group which later differentiated into distinct Hawaiian and Indonesian/California "branches". The number of compensatory base changes (CBCs) in the ITS2 indicated that the "Atlantic group", including the California isolate, constituted a single reproductive unit and that the Indonesian and Hawaiian T. weissflogii are two different biological species with regard to each other and to the "Atlantic clade". The beta-tubulin tree contradicts the reproductive units recovered by the compensatory base change analysis due to the close affinity of the California and Indonesia strains whereas the sexually induced gene 1 phylogeny supports the existence of three biological species, despite exhibiting a temporal sequence of geographic diversification that is different from that seen in topologies derived from the ribosomal RNA data. It is hypothesized that the tree derived from the sexually induced gene 1 reflects the relative order of the evolution of reproductive isolation in the different T. weissflogii strains while the lineages in the other phylogenies depict time elapsed since common ancestry. The current investigation is the first to have shown concordance in the pattern of variation between a reasonably good biological species marker (CBCs in the ITS2) and a protein hypothesized to be involved in sperm-egg recognition/adhesion in diatoms (Sig1). It was further discussed that the Pacific/Indonesian T. weissflogii species complex most likely evolved in the presence of gene flow and "local" environmental selection. Three hypotheses which potentially can explain the genetic diversification/similarity between the Atlantic T. weissflogii samples and the isolate obtained off the coast of California were proposed and discussed.
Abstract: Compensatory base changes (CBCs) in the ribosomal RNA (rRNA) internal transcribed spacer 2 (ITS2) secondary structures have been used to successfully verify the taxonomy of closely related species. CBCs have never been used to distinguish morphologically indistinct species. Under the hypothesis that CBCs will differentiate species in higher eukaryotes, novel software for CBC analysis was applied to morphologically indistinguishable insect species in the genus Altica. The analysis was species-specific for sympatric Altica beetles collected across four ecoregions and concordant with scanning electron microscopy data. This research shows that mining for CBCs in ITS2 rRNA secondary structures is an effective method for eukaryotic taxon analysis.
Abstract: Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.
Abstract: The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps.biozentrum.uni-wuerzburg.de) which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version, we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline. This allowed the identification of more than 160,000 correct full length and more than 50,000 partial structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses.
Abstract: ABSTRACT: BACKGROUND: In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. RESULTS: This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. CONCLUSIONS: Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion.Reviewers: This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin.
Abstract: ABSTRACT: BACKGROUND: Hypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously. FINDINGS: We built an accurate and in parts robustly resolved large scale phylogeny for 1,634 currently available hypnalean ITS2 sequence-structure pairs. CONCLUSIONS: Profile Neighbor-Joining revealed a possible hypnalean backbone, indicating that most of the hypnalean taxa classified as different moss families are polyphyletic assemblages awaiting taxonomic changes.
Abstract: The pennate planktonic diatom Pseudo-nitzschia delicatissima is very common in temperate marine waters and often responsible for blooms. Due to its surrounding rigid silicate frustrule the diatom undergoes successive size reduction as its vegetative reproduction cycle proceeds. Since a long time the life cycle of diatoms has raised scientific interest and some years ago extensive samples of Pseudo-nitzschia have been taken from coastal waters. Mating and cell size reduction experiments were carried out and served us as a data basis for a probabilistic model of cell size reduction. We applied a homogenous non-stationary continuous-time Markov chain to model the development of individual diatoms from an initial size of about 80mum until cell death which occurred when the size reached its low at about 18mum. In contrast to conventional curve fitting models we are capable of calculating confidence intervals for estimates of the population ages as well as integrate the process of auxospore formation into the model. We thus propose a unique way to describe the stationary size distribution in a diatom population in terms of cell division and auxospore formation probabilities of its individuals.
Abstract: The internal transcribed spacer 2 (ITS2) of the nuclear ribosomal repeat unit is one of the most commonly applied phylogenetic markers. It is a fast evolving locus, which makes it appropriate for studies at low taxonomic levels, whereas its secondary structure is well conserved, and tree reconstructions are possible at higher taxonomic levels. However, annotation of start and end positions of the ITS2 differs markedly between studies. This is a severe shortcoming, as prediction of a correct secondary structure by standard ab initio folding programs requires accurate identification of the marker in question. Furthermore, the correct structure is essential for multiple sequence alignments based on individual structural features. The present study describes a new tool for the delimitation and identification of the ITS2. It is based on hidden Markov models (HMMs) and verifies annotations by comparison to a conserved structural motif in the 5.8S/28S rRNA regions. Our method was able to identify and delimit the ITS2 in more than 30000 entries lacking start and end annotations in GenBank. Furthermore, 45000 ITS2 sequences with a questionable annotation were re-annotated. Approximately 30000 entries from the ITS2-DB, that uses a homology-based method for structure prediction, were re-annotated. We show that the method is able to correctly annotate an ITS2 as small as 58 nt from Giardia lamblia and an ITS2 as large as 1160 nt from humans. Thus, our method should be a valuable guide during the first and crucial step in any ITS2-based phylogenetic analysis: the delineation of the correct sequence. Sequences can be submitted to the following website for HMM-based ITS2 delineation: http://its2.bioapps.biozentrum.uni-wuerzburg.de.
Abstract: The rRNA cistron (18S-ITS1-5.8S-ITS2-28S) is used widely for phylogenetic analyses. Recent studies show that compensatory base changes (CBC) in the secondary structure of ITS2 correlate with genetic incompatibility between organisms. Rhizoctonia solani consists of genetically incompatible strain groups (anastomosis groups, AG) distinguished by lack of anastomosis between hyphae of strains. Phylogenetic analysis of internal transcribed spacer (ITS) sequences shows a strong correlation with AG determination. In this study, ITS sequences were reannotated according to the flanking 5.8S and 28S regions which interact during ribogenesis. One or two CBCs were detected between the ITS2 secondary structure of AG-3 potato strains as compared to AG-3 tobacco strains, and between these two strains and all other AGs. When a binucleate Rhizoctonia species related to Ceratobasidiaceae was compared to the AGs of R. solani, which were multinucleate (3-21 nuclei per cell), 1-3 CBCs were detected. The CBCs in potato strains of AG-3 distinguish them from AG-3 tobacco strains and other AGs yielding further evidence that the potato strains of AG-3 originally described as R. solani are a species distinct from other AGs. The ITS1-5.8S-ITS2 sequences were analyzed by direct sequencing of PCR products from 497 strains of AG-3 isolated from potato. The same 10 and 4 positions in ITS1 and ITS2, respectively, contained variability in 425 strains (86%). Nine different unambiguous ITS sequences (haplotypes) could be detected in a single strain by sequencing cloned PCR products indicating that concerted evolution had not homogenized the rRNA cistrons in many AG-3 strains. Importantly, the sequence variability did not affect the secondary structure of ITS2 and CBCs in AG-3.
Abstract: ABSTRACT: BACKGROUND: Current molecular phylogenetic studies of Lepidoptera and most other arthropods are predominantly based on mitochondrial genes and a limited number of nuclear genes. The nuclear genes, however, generally do not provide sufficient information for young radiations. ITS2, which has proven to be an excellent nuclear marker for similarly aged radiations in other organisms like fungi and plants, is only rarely used for phylogeny estimation in arthropods, although universal primers exist. This is partly due to difficulties in the alignment of ITS2 sequences in more distant taxa. The present study uses ITS2 secondary structure information to elucidate the phylogeny of a species-rich young radiation of arthropods, the butterfly subgenus Agrodiaetus. One aim is to evaluate the efficiency of ITS2 to resolve the phylogeny of the subgenus in comparison with COI, the most important mitochondrial marker in arthropods. Furthermore, we assess the use of compensatory base changes in ITS2 for the delimitation of species and discuss the prospects of ITS2 as a nuclear marker for barcoding studies. RESULTS: In the butterfly family Lycaenidae, ITS2 secondary structure enabled us to successfully align sequences of different subtribes in Polyommatini and produce a Profile Neighbour Joining tree of this tribe, the resolution of which is comparable to phylogenetic trees obtained with COI+COII. The subgenus Agrodiaetus comprises 6 major clades which are in agreement with COI analyses. A dispersal-vicariance analysis (DIVA) traced the origin of most Agrodiaetus clades to separate biogeographical areas in the region encompassing Eastern Anatolia, Transcaucasia and Iran. CONCLUSIONS: With the inclusion of secondary structure information, ITS2 appears to be a suitable nuclear marker to infer the phylogeny of young radiations, as well as more distantly related genera within a diverse arthropod family. Its phylogenetic signal is comparable to the mitochondrial marker COI. Compensatory base changes are very rare within Polyommatini and cannot be used for species delimitation. The implementation of secondary structure information into character-based phylogenetic methods is suggested to further improve the versatility of this marker in phylogenetic studies.
Abstract: The information that can be obtained from the secondary structure of the nuclear ribosomal internal transcribed spacer 2 (ITS2) is substantial, and yet many studies exploit this information inconsistently or inappropriately. This review introduces a remedy in the form of a flowchart where we detail the steps involved in estimating structure-based phylogenetic trees from ITS2 data. The pipeline described consists of the ITS2 Database, 4SALE, the CBCAnalyzer, and ProfDistS. Based on these tools, we describe how to utilize ITS2 sequence and secondary structure information together with an ITS2 specific scoring matrix and an ITS2 specific substitution model. The phylogenetic results thus obtained have been shown to be more reliable than approaches based on primary sequence data alone. Moreover, compensatory base changes (CBCs) in ITS2 sequence-structure pairs are identified as a possible marker for distinguishing species.
Abstract: MOTIVATION: The Profile Neighbor Joining (PNJ) algorithm as implemented in the software ProfDist is computationally efficient in reconstructing very large trees. Besides the huge amount of sequence data the structure is important in RNA alignment analysis and phylogenetic reconstruction. RESULTS: For this ProfDistS provides a phylogenetic workflow that uses individual RNA secondary structures in reconstructing phylogenies based on sequence-structure alignments - using Profile Neighbor Joining (PNJ) with manual or iterative and automatic profile definition. Moreover, ProfDistS can deal also with protein sequences. AVAILABILITY: ProfDistS is freely available for non-commercial use for Windows, Linux and MAC operating systems at http://profdist.bioapps.biozentrum.uni-wuerzburg.de. CONTACT: tobias.mueller@biozentrum.uni-wuerzburg.de, matthias.wolf@biozentrum.uni-wuerzburg.de.
Abstract: ABSTRACT: BACKGROUND: The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There are several tools available that help performing these tasks, but all of them are specialized and focus on only one aspect, editing the alignment or plotting the secondary structure. The problem is both these tasks need to be performed simultaneously. FINDINGS: 4SALE is designed to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary structure information, 4SALE enables to improve and understand RNA sequence and secondary structure evolution much more easily. CONCLUSION: 4SALE is a step further for simultaneously handling RNA sequence and secondary structure information. It provides a complete new way of visual monitoring different structural aspects, while editing the alignment. The software is freely available and distributed from its website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de/
Abstract: BACKGROUND: Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment. RESULTS: The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae. CONCLUSION: In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics.
Abstract: An increasing number of phylogenetic analyses are based on the internal transcribed spacer 2 (ITS2). They mainly use the fast evolving sequence for low-level analyses. When considering the highly conserved structure, the same marker could also be used for higher level phylogenies. Furthermore, structural features of the ITS2 allow distinguishing different species from each other. Despite its importance, the correct structure is only rarely found by standard RNA folding algorithms. To overcome this hindrance for a wider application of the ITS2, we have developed a homology modelling approach to predict the structure of RNA and present the results of modelling the ITS2 in the ITS2 Database. Here, we describe the database and the underlying algorithms which allowed us to predict the structure for 86 784 sequences, which is more than 55% of all GenBank entries concerning the ITS2. These are not equally distributed over all genera. There is a substantial amount of genera where the structure of nearly all sequences is predicted whereas for others no structure at all was found despite high sequence coverage. These genera might have evolved an ITS2 structure diverging from the standard one. The current version of the ITS2 Database can be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de.
Abstract: It was shown that compensatory base changes (CBCs) in internal transcribed spacer 2 (ITS2) sequence-structure alignments can be used for distinguishing species. Using the ITS2 Database in combination with 4SALE - a tool for synchronous RNA sequence and secondary structure alignment and editing - in this study we present an in-depth CBC analysis for placozoan ITS2 sequences and their respective secondary structures. This analysis indicates at least two distinct species in Trichoplax (Placozoa) supporting a recently suggested hypothesis, that Placozoa is âno longer a phylum of oneâ.
Abstract: We reconstructed a robust phylogenetic tree of the Metazoa, consisting of almost 1,500 taxa, by profile neighbor joining (PNJ), an automated computational method that inherits the efficiency of the neighbor joining algorithm. This tree supports the one proposed in the latest review on metazoan phylogeny. Our main goal is not to discuss aspects of the phylogeny itself, but rather to point out that PNJ can be a valuable tool when the basal branching pattern of a large phylogenetic tree must be estimated, whereas traditional methods would be computationally impractical.
Abstract: Given two organisms, how can one distinguish whether they belong to the same species or not? This might be straightforward for two divergent organisms, but can be extremely difficult and laborious for closely related ones. A molecular marker giving a clear distinction would therefore be of immense benefit. The internal transcribed spacer 2 (ITS2) has been widely used for low-level phylogenetic analyses. Case studies revealed that a compensatory base change (CBC) in the helix II or helix III ITS2 secondary structure between two organisms correlated with sexual incompatibility. We analyzed more than 1300 closely related species to test whether this correlation is generally applicable. In 93%, where a CBC was found between organisms classified within the same genus, they belong to different species. Thus, a CBC in an ITS2 sequence-structure alignment is a sufficient condition to distinguish even closely related species.
Abstract: We have converted the hierarchically organized new higher level classification of eukaryotes with emphasis on the taxonomy of protists proposed by Adl et al. into an interactive and dynamic Java applet. The current version of the applet can be accessed via http://phylogenetics.bioapps.biozentrum.uni-wuerzburg.de/etv. We use the layout from a Degree-of-Interest tree (DOITree) that effectively displays all the taxonomic information as well as the phylogenetic relationships described in the original article by Adl et al. The tree was made using the Prefuse Toolkit for interactive information visualization. All browsers capable of using Java applets will be able to view the tree. The applet is freely available for scientists, teachers, and students.
Abstract: The internal transcribed spacer 2 (ITS2) is a phylogenetic marker which has been of broad use in generic and infrageneric level classifications, as its sequence evolves comparably fast. Only recently, it became clear, that the ITS2 might be useful even for higher level systematic analyses. As the secondary structure is highly conserved within all eukaryotes it serves as a valuable template for the construction of highly reliable sequence-structure alignments, which build a fundament for subsequent analyses. Thus, any phylogenetic study using ITS2 has to consider both sequence and structure. We have integrated a homology based RNA structure prediction algorithm into a web server, which allows the detection and secondary structure prediction for ITS2 in any given sequence. Furthermore, the resource contains more than 25,000 pre-calculated secondary structures for the currently known ITS2 sequences. These can be taxonomically searched and browsed. Thus, our resource could become a starting point for ITS2-based phylogenetic analyses and is therefore complementary to databases of other phylogenetic markers, which focus on higher level analyses. The current version of the ITS2 database can be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de.
Abstract: BACKGROUND: In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously. RESULTS: 4SALE fills this gap. The application allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis. CONCLUSION: 4SALE, which provides an user-friendly and intuitive interface, is a comprehensive toolbox for RNA analysis based on sequence and secondary structure information. The program connects sequence and structure databases like the ITS2 Database to phylogeny programs as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore platform independent. The software is freely available and distributed from the website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de.
Abstract: SUMMARY: ProfDist is a user-friendly software package using the profile-neighbor-joining method (PNJ) in inferring phylogenies based on profile distances on DNA or RNA sequences. It is a tool for reconstructing and visualizing large phylogenetic trees providing new and standard features with a special focus on time efficency, robustness and accuracy. AVAILABILITY: A Windows version of ProfDist comes with a graphical user interface and is freely available at http://profdist.bioapps.biozentrum.uni-wuerzburg.de
Abstract: The hydrodictyacean green algal lineage has been the focus of much research due to the fossil record of at least some members, their ornamented cell walls, and their distinctive reproductive strategies. The phylogeny of the family was, until recently, exclusively morphology based. This investigation examines hydrodictyacean isolates from several culture collections, focusing on sequences from ribosomal data: 18S rDNA, 26S rDNA (partial), and internal transcribed spacer (ITS)-2 data. Results from phylogenetic analyses of independent and combined data matrices support the Hydrodictyaceae as a monophyletic lineage that includes isolates of Chlorotetraedron, Hydrodictyon, Pediastrum, Sorastrum, and Tetraedron. Phylogenetic analyses of rDNA data indicate that the three-dimensional coenobium of Hydrodictyon is evolutionarily distinct from the three-dimensional coenobium of Sorastrum. The more robust aspects of the ITS-2 data corroborate the 18Sþ26S rDNA topology and provide a structural autapomorphy for the Hydrodictyaceae and Neochloridaceae, that is, an abridgment of helix IV in the secondary structure. The rDNA data do not support monophyly of Pediastrum but rather suggest the existence of four additional hydrodictyacean genera: Monactinus, Parapediastrum, Pseudopediastrum, and Stauridium.
Abstract: The ongoing characterization of novel species creates the need for a molecular marker which can be used for species- and, simultaneously, for mega-systematics. Recently, the use of the internal transcribed spacer 2 (ITS2) sequence was suggested, as it shows a high divergence in sequence with an assumed conservation in structure. This hypothesis was mainly based on small-scale analyses, comparing a limited number of sequences. Here, we report a large-scale analysis of more than 54,000 currently known ITS2 sequences with the goal to evaluate the hypothesis of a conserved structural core and to assess its use for automated large-scale phylogenetics. Structure prediction revealed that the previously described core structure can be found for more than 5000 sequences in a wide variety of taxa within the eukaryotes, indicating that the core secondary structure is indeed conserved. This conserved structure allowed an automated alignment of extremely divergent sequences as exemplified for the ITS2 sequences of a ctenophorean eumetazoon and a volvocalean green alga. All classified sequences, together with their structures can be accessed at http://www.biozentrum.uni-wuerzburg.de/bioinformatik/projects/ITS2.html. Furthermore, we found that, although sample sequences are known for most major taxa, there exists a profound divergence in coverage, which might become a hindrance for general usage. In summary, our analysis strengthens the potential of ITS2 as a general phylogenetic marker and provides a data source for further ITS2-based analyses.
Abstract: The CBCAnalyzer (CBC=compensatory base change) is a custom written software toolbox consisting of three parts, CTTransform, CBCDetect, and CBCTree. CTTransform reads several ct-file formats, and generates a so called "bracket-dot-bracket" format that typically is used as input for other tools such as RNAforester, RNAmovie or MARNA. The latter one creates a multiple alignment based on primary sequences and secondary structures that now can be used as input for CBCDetect. CBCDetect counts CBCs in all against all of the aligned sequences. This is important in detecting species that are discriminated by their sexual incompatibility. The count (distance) matrix obtained by CBCDetect is used as input for CBCTree that reconstructs a phylogram by using the algorithm of BIONJ. In this note we describe the features of the toolbox as well as application examples. The toolbox provides a graphical user interface. It is written in C++ and freely available at: http://cbcanalyzer.bioapps.biozentrum.uni-wuerzburg.de.
Abstract: 18S ribosomal DNA and internal transcribed spacer 2 (ITS-2) full-length sequences, each of which was sequenced three times, were used to construct phylogenetic trees with alignments based on secondary structures, in order to elucidate genealogical relationships within the Aplysinidae (Verongida). The first poriferan ITS-2 secondary structures are reported. Altogether 11 Aplysina sponges and 3 additional sponges (Verongula gigantea, Aiolochroia crassa, Smenospongia aurea) from tropical and subtropical oceans were analyzed. Based on these molecular studies, S. aurea, which is currently affiliated with the Dictyoceratida, should be reclassified to the Verongida. Aplysina appears as monophyletic. A soft form of Aplysina lacunosa was separated from other Aplysina and stands at a basal position in both 18S and ITS-2 trees. Based on ITS-2 sequence information, the Aplysina sponges could be distinguished into a single Caribbean-Eastern Pacific cluster and a Mediterranean cluster. The species concept for Aplysina sponges as well as a phylogenetic history with a possibly Tethyan origin is discussed.
Abstract: Structural genomics meets phylogenetics and vice versa: Knowing rRNA secondary structures is a prerequisite for constructing rRNA alignments for inferring phylogenies, and inferring phylogenies is a precondition to understand the evolution of such rRNA secondary structures. Here, both scientific worlds go together. The rRNA internal transcribed spacer 2 (ITS2) region is a widely used phylogenetic marker. Because of its high variability at the sequence level, correct alignments have to take into account structural information. In this study, we examine the extent of the conservation in structure. We present (1) the homology modeled secondary structure of more than 20,000 ITS2 covering about 14,000 species; (2) a computational approach for homology modeling of rRNA structures, which additionally can be applied to other RNA families; and (3) a database providing about 25,000 ITS2 sequences with their associated secondary structures, a refined ITS2 specific general time reversible (GTR) substitution model, and a scoring matrix, available at http://its2.bioapps.biozentrum.uni-wuerzburg.de.
Abstract: Chlorella is one of the archetypical forms of coccoid green algae and one of the best-studied phototrophic eukaryotes. However, its systematics remains enigmatic due to conflicts between morphological and molecular phylogenetical approaches. The sequences of the 18S rRNA gene of nine strains of Chlorella and related taxa, and the ITS2-region of 17 strains of Chlorellaceae were studied and included in phylogenetic analyses. The secondary structure of the ITS2-region of Chorella vulgaris was compared to that of Parachlorella beyerinckii. All phylogenetic analyses showed that the Chlorellaceae form a clade within the Trebouxiophyceae. The Chlorellaceae studied here are divided into two sister groups: (i) the Parachlorella clade with Parachlorella beyerinckii gen. et spec. nov. and Parachlorella kessleri comb. nov. as well as Dicloster acuatus and Closteriopsis acicularis, and (ii) the Chlorella clade including the âtrueâ spherical Chlorella species C. vulgaris, C. lobophora and C. sorokiniana. The latter are intermixed with taxa that differ in morphology and were formerly classified in other families of coccoid green algae: Actinastrum hantzschii (formerly Coelastraceae), Diacanthos belenophorus (formerly Oocystaceae), Dictyosphaerium pulchellum (formerly Botryococcaceae), Didymogenes anomala and D. palatina (formerly Scenedesmaceae) and Micractinium pusillum (formerly Micractiniaceae). It was shown that morphological criteria traditionally used for classification (e.g. spines, mucilaginous envelopes, or the formation of colonies or coenobia) are burdened with a high degree of phenotypic plasticity. These plastic traits represent adaptations to environmental factors in order to optimize floating in the water column and to resist against grazing pressure. A genus and species concept in Chlorellaceae remains provisional, because, in most cases, there is still a lack of classical and molecular approaches to identify clear phylogenetic lineages.
Abstract: The phylogenetic position of the Mollicutes has been re-examined by using phosphoglycerate kinase (Pgk) amino acid sequences. Hitherto unpublished sequences from Mycoplasma mycoides subsp. mycoides, Mycoplasma hyopneumoniae and Spiroplasma citri were included in the analysis. Phylogenetic trees based on Pgk data indicated a monophyletic origin for the Mollicutes within the Firmicutes, whereas Bacilli (Firmicutes) and Clostridia (Firmicutes) appeared to be paraphyletic. With two exceptions, i.e. Thermotoga (Thermotogae) and Fusobacterium (Fusobacteria), which clustered within the Firmicutes, comparative analyses show that at a low taxonomic level, the resolved phylogenetic relationships that were inferred from both the Pgk protein and 16S rRNA gene sequence data are congruent.
Abstract: Sequence variation of the ribosomal DNA internal transcribed spacer II (ITS2) among species of the diatom genus Stephanodiscus was investigated by Zechman et al. (1994). In addition, Zechman et al. (1994) sequenced a repeat from Cyclotella meneghiniana to determine the taxonomic range over which the ITS2 region could be used for diatom systematics. It was mentioned that, for Cyclotella, much of the ITS2 region was not alignable with that for Stephanodiscus species, and therefore, a generic-level comparison within the Thalassiosiraceae may not be possible, i.e., only interspecific relationships could be assessed with ITS2 sequences. In this study secondary structures of the ITS2 transcript in Cyclotella and Stephanodiscus were derived. The secondary structure seemed to be more conservative than the primary sequence. The higher-order structure shares conservation patterns, e.g., with green algae and flowering plants. However, Cyclotella could be used as an outgroup for rooting a phylogenetic tree concerning sister group relations within Stephanodiscus. Therefore, it is shown that Stephanodiscus neoastraea is closely related to S. hantzschii and not, as previously proposed, to the Stephanodiscus-niagarae-complex.
Abstract: BACKGROUND: In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimated by the usual methods (maximum parsimony (MP), neighbor-joining (NJ), or maximum likelihood (ML)), nor are they well supported. We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades. RESULTS: Our estimator of profile distances generalizes the maximum likelihood estimator of sequence distances. The basal branching pattern can be estimated by any distance-based method, such as neighbor-joining. Our method (profile neighbor-joining, PNJ) then inherits the accuracy and robustness of profiles and the time efficiency of neighbor-joining. CONCLUSIONS: Phylogenetic analysis of Chlorophyceae with traditional methods (MP, NJ, ML and MrBayes) reveals seven well supported subclades, but the methods disagree on the basal branching pattern. The tree reconstructed by our method is better supported and can be confirmed by known morphological characters. Moreover the accuracy is significantly improved as shown by parametric bootstrap.
Abstract: Due to the significant lack of information on the community structure of deep-sea nanoflagellates and other nanofauna components as a potentially important component of deepsea matter fluxes, the aim of the present study was to check whether there is a specific deep-sea nanofauna (<20 µm) community. Studies were carried out in the deep oligotrophic basins of the Eastern Mediterranean Sea around Greece (1249 to 4260 m depth). Direct microscopic counts and quantitative cultivation techniques were used to estimate the abundance and community structure of heterotrophic flagellates and amoebae from abyssopelagial samples and deep-sea sediments. Euglenids and bodonids were the dominant groups comprising about 2/3 of the abundance and biomass of flagellate nanofauna. Our direct counts clearly demonstrate that attention also has to be paid to species which seldom appear in crude cultures. The records of hemimastigid-like forms were remarkable in this respect. Among the 35 deep-sea nanofauna taxa identified here, 8 never appeared in cultures and 18 taxa were found only in cultures. At least 9 taxa have not been previously recorded from the deep sea. Meteora sporadica seems to be the first record of an endemic deep-sea heterotrophic nanoprotist. The variety of functional groups recorded indicates the nanofauna as part of a complex microbial food web in the deep sea. Estimates of potential maximum growth rates of fresh isolates from deep-sea waters ranged from 1 to 6.3 dâ1 (Ancyromonas, Amastigomonas, Bodo, Caecitellus, Cafeteria, Kiitoksia, Massisteria, Percolomonas). There was considerable clonal variability.
Abstract: The complete 18S rDNA and ITS-2 sequences of two strains of Scenedesmus arcuatus were determined and subjected to phylogenetic analyses. Furthermore, ITS-2 sequences of Scenedesmus obtusus, of S. hindakii, and of Acutodesmus regularis were investigated. Phylogenetic analyses indicated that S. hindakii is most closely related to S. raciborskii and/or S. obtusus, embedded in the Scenedesmus cluster. The morphologically similar S. arcuatus and its variety platydiscus branched outside the Scenedesmus/Acutodesmus cluster (18S) or together with A. regularis and A. pectinatus (ITS-2). Therefore, the genera Acutodesmus and/or Scenedesmus are paraphyletic. S. arcuatus is not closely related to S. hindakii.
Abstract: The systematics of coccoid green algae is going through a dramatic phase of change. Classical approaches using morphological characters for the circumscription of taxa do not adequately reflect the phylogenetic relationships. Molecular data provide new insights into the phylogeny of coccoid Chlorophyta. Whereas the content of the orders Chlorococcales and Chlorellales needs to be reduced, the order Sphaeropleales comprises more families than in the traditional circumscription. According to molecular biological investigations the Neochloridaceae, Selenastraceae and Scenedesmaceae, formerly classified within the Chlorococcales and later within the Chlorellales, belong to the Sphaeropleales. The Hydrodictyaceae, formerly a member of the Protosiphonales, are also to be classified in the Sphaeropleales. Some former members of the Ulotrichales, which propagate by binary fission, cluster together with autosporine coccoid taxa within the Chlorellales, Trebouxiophyceae. In this study, by presenting six new 18S rRNA gene sequences of chlorophytes we scroll through a phylogenetic tree that contains the main evolutionary lineages of the Chlorophyta, and we take up diffrent topics of current interest for green algal systematists. (1) Chlorococcum robustum, formerly a member of the Chlorococcales s. str. is shown to be closely related to Chlamydopodium vacuolata; both belong to the Chlamydomonadales. (2) Pectodictyon pyramidale, formerly grouped with the Radiococcaceae, is closely related to Coelastrum reticulatum and both, like other coelastracean taxa, belong to the Scenedesmaceae, Sphaeropleales. (3) Pseudodictyosphaerium jurisii is a member of the Mychonastes clade containing picoplanktonic taxa. This clade is sister group to the Oedogoniales at the base of the Chlorophyceae. A new order will need to be established eventually to accommodate this clade. Whereas the position of (4) Lagerheimia genevensis within the Oocystaceae was confirmed, the former crucigenoid species (5) Crucigeniella rectangularis is to be transferred to this family. The latter two taxa demonstrate that the morphological diversity in the Oocystaceae is wider than expected. This observation is discussed in comparison to the family Chlorellaceae. (6) Catena viridis a former member of the Ulotrichales belongs to the Chlorellales, Trebouxiophyceae.
Abstract: The 18S rRNA gene sequences of three strains of Radiococcus polycoccus, one strain of Planktosphaeria gelatinosa and one strain of Schizochlamydella capsulata (Radiococcaceae, Chlorophyta) were determined and subjected to phylogenetic analyses. Cladistic as well as likelihood analyses indicated that Radiococcus polycoccus and Planktosphaeria gelatinosa are closely related within the Sphaeropleales (Chlorophyceae), while Schizochlamydella capsulate clustered with Amphikrikos spec. within the Oocystaceae (Trebouxiophyceae). Neither R. polycoccus nor P. gelatinosa or S. capsulata are related to Coenocystis inconstans, the only member of Radiococcaceae of which the 18S rRNA gene sequence was known earlier. The results give _rst impression that the Radiococcaceae could be a polyphyletic assemblage of coccoid mucilage forming chlorophytes.
Abstract: Chlorococcalean algae exhibiting globular cells and having spiny projections on their cell walls are currently classi_ed within the family Micractiniaceae and Golenkiniaceae. We studied the phylogenetic relationships of Golenkinia to other spine-bearing chlorococcal algae using a phylogenetic analysis of molecular marker gene sequences. The 18S rRNA gene sequences of three strains of Golenkinia (Golenkiniaceae) and one strain of Micractinium (Micractiniaceae), were determined and subjected to a phylogenetic analysis algorithm. This phylogenetic analysis indicated that the Golenkiniaceae represent an independent lineage at the basis of the Chlamydomonadales (Chlorophyceae). This observation does not support previous classi_cations in which, Golenkinia is grouped together with Polyedriopsis (Sphaeropleales). The genus Micractinium is paraphyletic and is closely related to Chlorella (Trebouxiophyceae).
Abstract: Actinastrum hantzschii LAGERHEIM is characterized by spindle-shaped cells that are truncated at one end and arranged 3-dimensionally in colonies. An isolate of the alga was characterized by the use of light and electron microscopy as well as 18S rRNA gene sequencing. Despite morphological differences, phylogenetic analyses indicated that A. hantzschii is closely related to the trebouxiophycean taxa Chlorella sorokiniana SHIHIRA et KRAUS, C. vulgaris BEIJERINCK and C. lobophora ANDREYEVA, and did not show an affinity to the Scenedesmaceae as previously proposed. Previous studies on Closteriopsis acicularis G. M. SMITH (Trebouxiophyceae), together with the findings of the present study, question the concept of "Chlorella sensu stricto" as well as the criteria currently used in the systematics of coccoid green algae.
Abstract: The complete 18S rRNA gene sequences of four Sphaeroplea C.A. AGARDH strains (Sphaeropleales, Sphaeropleaceae), two Atractomorpha HOFFMANN strains (Sphaeropleales, Sphaeropleaceae) and two Ankyra (KORSHIKOV) FOTT strains (Chlorococcales, Characiaceae) were determined and subjected to phylogenetic analysis algorithms. Cladistic analyses indicated that all these taxa belong to a monophyletic lineage (Sphaeropleaceae) and are related to a group of chlorophycean algae comprising autosporic taxa and taxa that reproduce by zoospores which are characterized by directly opposed basal bodies. The taxonomic assignment of the Sphaeropleaceae as a family within the Sphaeropleales (Chlorophyta, Chlorophyceae) is discussed.
Abstract: Stephanodiscus neoastraea Hakansson et Hickel is distinguished from S. heterostylus Hakansson et Meyer by the absence of valve face fultoportulae. Scanning electron microscopy analyses (SEM) revealed, that cultures established from a single cell of S. neoastraea and/or S. heterostylus persistently contained a mixture of organisms with and without valve face fultoportulae. Amplification of the ITS2 spacer region of the nuclear encoded rRNA transcription unit yielded a single band in an agarose gel electrophoresis for three "mixed" cultures tested. Furthermore, sequencing of the ITS2 region resulted in unambiguous sequences that were identical for each strain investigated. Ambiguous peaks which may originate from sequencing a mixture of different templates did not appear in the electropherogram. Thus, no, one or several valve face fultoportulae appear in the same species. Absence or presence of fultoportulae is not a useful character for differentiating S. neoastraea and S. heterostylus. Presence or absence of tubular processes at the valve face is a variable character, clearly expressed in clonal culture, and thus cannot be used for species discrimination. The species name S. heterostylus is a ânomen nudumâ, and thus invalid.
Abstract: The methanogenic archaeal communities in the sediment of two basins of an artificially partitioned acidic bog lake were studied. In the northeast basin, which was separated from a peat bog, a high methane production rate was measured only in the upper layers of the sediment. In contrast, methane production was detected at various depths of the sediment in the southwest basin, which continuously receiving humic acids from the bog. Ten bands were observed in the denaturing gradient gel electrophoresis (DGGE) fingerprint of the 16S rDNA archaeal amplicons from the NE basin top (0^5 cm) sediment layer, which reflected the presence of at least 10 ribotypes. Seventy clones of the 16S rDNA amplicons were obtained from the NE basin top sediment layer, and were grouped into 10 operational taxonomy units (OTUs) according to their positions on the DGGE gel. Seven of these OTUs could be matched with the bands of the community fingerprint. Phylogenetic analyses indicated that the sequences clustered into three groups: five of the OTUs were related to Methanosaeta, four OTUs to Methanomicrobiales and one OTU to Methanobacterium. Among the OTUs, sequences with high similarities (s96%) were retrieved. The sequence data suggested that the diversity of the methanogenic archaeal community was limited. Bands corresponding to those three phylogenetic groups were found in the DGGE fingerprints of both NE and SW basins, which reflected the presence of the same dominant methanogenic archaeal groups in both basins. However, differences in the distribution of the ribotypes that had high 16S rRNA sequence identities were observed in the fingerprints between the two basins at various depths. The microdiversity decreased along the sediment depth in the NE basin, and vice versa in the SW basin. The greater variety of the archaeal ribotypes, apparently, correlated with the higher methanogenesis rate.
Abstract: The deep sea covers more than 90% of the ocean floor. Nevertheless, the knowledge of deep sea organisms â especially of protozoa â is scarce and many species found there are probably still undescribed. During sampling in the Sporades Basin (Mediterranean Sea), a new extraordinary protozoan species was found in sediments at a depth of 1,230 m. Meteora sporadica gen. nov. et sp. nov. is a small (cell body length between 3.0 and 4.4 μm) protist possessing two axial cell appendages and two characteristic lateral arms which perform almost continual rowing movements. Its morphology is unlike that of any other higher order taxon. Therefore, the new genus was classified as Protista incertae sedis.
Abstract: In order to understand protozoology from the perspective of science theory and biophilosophy, the history and the concept of protozoology have been analysed. To this end, almost 40 protozoologists were taken into consideration and correlated with distinct phases in the evolution of the discipline. Names, lifespans and events were combined into one picture to identify individuals representative of each step in the genesis of protozoology. On the basis of who could have known whom and who could have known what, their different concepts have been interpreted. The evolving terminology, in particular, has generated a species-concept for taxonomy, systematics and classification which is new for almost all protozoologist and therefore of special interest for modern protozoology. Additionally, by the analysis of protozoological congresses a general â qualitative and quantitative â profile of the history and concept of traditional and modern protozoology has been developed and here presented and discussed.
Abstract: In this study, we present the possibilities for calculating systematic relationships on higher taxonomical levels based exclusively on ITS1. This is demonstrated for Boraginales (Boraginaceae s.str., Cordiaceae, Ehretiaceae, Heliotropiaceae, Hydrophyllaceae and Lennoaceae). Secondary structure of the ITS1 region is more conserved than the primary structure (i.e., sequence itself) and is therefore a tool for optimizing alignments. It increases the number of structural characters. Information inferred from the secondary structure enables us to construct well-resolved phylogenetic trees at higher taxonomic levels. A general secondary structure of ITS1 for Boraginales, with four major helices, is proposed here. In each subtaxon, derivations from this structure are found. The paraphyly of Boraginaceae s.l. is evident from both a comparison of secondary structures and from bootstrap analysis. Boraginaceae s.str. are the sister group of a clade formed by Hydrophyllaceae, Cordiaceae, Ehretiaceae, Heliotropiaceae and Lennoaceae. The last four taxa constitute a monophyletic group which is the sister group of Hydrophyllaceae. Lennoaceae are closely related to Ehretiaceae, and these two taxa in turn are the sister group of Cordiaceae.
Abstract: We investigated unialgal strains of the type species of the genera Chlorotetraedron and Polyedriopsis, C. polymorphum and P. spinulosa, and also of C. incus, by means of 18S rRNA analyses. According to the phylogenetic analyses, C. incus, C. polymorphum and P. spinulosa are closely related and belong to the Chlorophyceae, family Neochloridaceae; this contrasts with the previous classification of Polyedriopsis in the Golenkiniaceae.
Abstract: Ist jemand kein "studierter" Biologe, möchte sich aber gerne intensiver mit dieser naturwissenschaftliche Disziplin, insbesondere mit der zoologischen und/oder botanischen Taxonomie/Systematik auseinandersetzen, wird er sich den entsprechenden Fachbüchern zuwenden. Mit einiger Sicherheit werden - nach anfänglicher Begeisterung - in ihm, wenn er mehr als ein Buch zu Rate zieht, Zweifel über den Aussagewert der, wie er hoffte, kompetenten Literatur aufkommen. Es kann nämlich sehr leicht passieren, daà er, wenn er beispielsweise in zwei Zoologiebüchern (Storch und Welsch, 1997; Westheide und Rieger, 1996) und einem Botaniklehrbuch (Sitte et al., 1998) (oder einer anderen, beliebigen Buchkombination aus beiden Fachdisziplinen) die Ausführungen zum System der Tiere/Pflanzen liest, drei (oder mehr) zunächst grundverschieden anmutende Variationen zu dieser Thematik vorfindet. Woran mag dies liegen? Sicherlich nicht am verschiedenen Alter der Bücher, denen möglicherweise ein jeweils anderer Wissensstand zugrunde liegen könnte. Nein, alle sind innerhalb der letzten drei Jahre ausgewiesenermaÃen als aktuelle Auflagen erschienen. Im Folgenden soll versucht werden, das Problem zu entflechten und aufzuzeigen, wo die Schwierigkeiten, die letzlich zu einer Art babylonischer Sprachverwirrung führen, ihre Wurzeln haben.
Abstract: Bildung, so schreibt 1912 Raoul Heinrich France, der Gründer des MIKROKOSMOS, ist die Fähigkeit, sich in Harmonie mit dem Weltall zu setzen, und wer Bildung sucht, dem ist die Pflanze ein Helfer. Volkstümlich, heute würden wir sagen populärwissenschaftlich, über sie zu schreiben, ist ihm - im besten Sinne - ein Schauspiel, ein Theater, eine symbolische Komödie von jenen Geheimnissen des Lebens. Er erkannte die Sackgasse eines Linneismus, einer in spanischen Stieflen eingezwängten Wissenschaft und er wollte - seiner Zeit voraus - die Welt der Pflanzen eben nicht nur beschreiben, sondern die Botanik als Bildungsmittel erneuern und verstanden wissen. Dabei kennzeichnet - in Anlehnung an die Wortwahl von France - die "Tierwerdung der Pflanze" eine Botanik und Zoologie zwischen Karneval und Aschermittwoch.
Abstract: The goal of phylogenetics is to reconstruct ancestral relationships between different taxa, e.g., different species in the tree of life, by means of certain characters, such as genomic sequences. We consider the prominent problem of reconstructing the basal phylogenetic tree topology when several subclades have already been identified or are well known by other means, such as morphological characteristics. Whereas most available tools attempt to estimate a fully resolved tree from scratch, the profile neighbor-joining (PNJ) method focuses directly on the mentioned problem and has proven a robust and efficient method for large-scale data sets, especially when used in an iterative way. We describe an implementation of this idea, the ProfDist software package, which is freely available, and apply the method to estimate the phylogeny of the eukaryotes. Overall, the PNJ approach provides a novel effective way to mine large sequence datasets for relevant phylogenetic information.
