- since 02/2011 Young Investigator Group Leader, DNA Analytics Core Facility, University of Würzburg - 04/2008-10/2010 PhD Student, BIGSS Bavarian Elite Graduate Network - 11/2007-10/2010 PhD Student, Department of Bioinformatics, University of Würzburg - 03/2010-04/2010 Visiting Scientist, Department of Biology, Edinboro University, PA, USA - 06/2007-10/2010 Research Assistant, Dept. of Animal Ecology and Tropical Biology, University of Würzburg - 05/2007-06/2007 Field Assistant, Surveying and mapping of Cricetus cricetus, FABION Gbr - 07/2006-10/2006 Visiting Scientist, Department of Biology, University Brunei Darussalam - 05/2005-08/2005 Visiting Scientist, Hitoy Cerere National Park, Costa Rica - 04/2004-05/2007 Graduate student (MSc), Dept. of Animal Ecology and Tropical Biology, University of Würzburg - 10/2001-04/2004 Undergraduate student (BSc), University of Karlsruhe
Service as Reviewer: Biological Conservation (2011), BMC Evolutionary Biology (2008), BMC Research Notes (2011), Canadian Journal of Zoology (2010), Herpetological Journal (2010), Journal of Evolutionary Biology (2010), Journal of Zoological Systematics and Evolutionary Research (2010), Molecular Phylogenetics and Evolution (2008, 2009, 2010, 2011), PLoS One (2011), Zoologia (2010)
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: 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: With integration of secondary structures, ribosomal genes have once again become very popular for phylogenetic analyses. This additional source of information to the nucleotide sequence provides a massive boost for taxonomic inferences. Herein, we propose that in the near future a further benefit for phylogenetics with such genes will be very likely by inclusion of the third dimension. For the first time, we determined the tertiary structure of the ribosomal internal transcribed spacer 2 for Chlamydomonas rheinhardtii by application of two different in silico prediction algorithms. We compared these methods with focus on phylogenetic usability. Further, we determined the tertiary structures for closely related green algae to provide a small phylogenetic example. The results suggest that the tertiary structure inherits evolutionary information observable neither within the sequence nor in the secondary structure.
Abstract: Sequences and secondary structures of the nuclear-encoded internal transcribed spacer 2 (ITS2) ribosomal RNA of nine
Coelastrum taxa, Asterarcys quadricellulare (Coelastraceae), Westella botryoides (hitherto Oocystaceae) and Dimorphococcus
lunatus (Scenedesmaceae) were determined and compared with existing GenBank entries of scenedesmacean taxa
(Desmodesmus, Enallax, Neodesmus, Scenedesmus). Phylogenetic analyses showed that the studied Coelastrum taxa
belong to several different lineages within the Scenedesmaceae: five Coelastrum taxa (Coelastrum microporum, Coelastrum
astroideum, C. astroideum var. rugosum 5 Coelastrum rugosum, Coelastrum pseudomicroporum and Coelastrum
sphaericum incl. Coelastrum proboscideum) form monophyletic clades, whereas two strains labeled Coelastrum morum
belong to different genera. The African strain of C. morum clusters with Coelastrum cambricum. The Finnish strain
labeled C. morum clusters with Asterarcys, Dimorphococcus and Hariotina. According to its morphology this strain
belongs to Coelastrella, related to Coelastrella saiponensis. Westella botryoides belongs to a separate clade within the
Scenedesmaceae. Coelastrum reticulatum is positioned in the clade with Asterarcys, Dimorphococcus and Coelastrella;
hence its separation in a separate genus, as originally described (Hariotina), is justified. In general, the phylogenetic
analysis of ITS2 data shows that the Coelastraceae are included in the monophyletic Scenedesmaceae, and thus the
splitting into two families is not justified, but they belong to the monophyletic subfamily Coelastroidea. The genera
Comasiella and Pectinodesmus are newly erected, and several new combinations are proposed.
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: We investigated the amphibian species richness within the Ulu Temburong National Park,
Brunei Darussalam. Standardized visual and acoustic transect sampling and encounter surveys were
conducted from April 2005 â October 2006. We identiï¬ed a total of 54 amphibian species, 53 frogs and
1 caecilian. 15 species were new records for the park while 12 were new records for Brunei Darussalam.
This brings the total number of amphibian species in Ulu Temburong to 66 species. Robust abundance
measures are provided for 42 of the 66 species. Two-thirds of the regional, lowland and hilly forest frog
diversity of Borneo was found within 25 km2 of the Ulu Temburong National Park. This is a remarkable
percentage, suggesting that this site deserves high conservation priority. High species richness is likely to
result from the high diversity of breeding habitats and the conï¬uence of the regional faunas of two bio-
geographical units in Borneo: East Sarawak and the hilly heart of Borneo.
Abstract: 1. Several hypotheses have been proposed to explain the structure of multi-species assemblages. Among these, abiotic environmental factors and biotic processes are often favoured. Several recent studies examining anuran communities identified environmental factors to be only of minor importance in the composition of leaf-litter and canopy assemblages in pristine forests. Instead, spatial effects and spatially structured environments were considered more important.
2. In this study, we investigated whether these findings could also be confirmed for very heterogeneous stream habitats in the primary rainforest of the Ulu Temburong National Park, Brunei Darussalam. We thus investigated anuran assemblage compositions on 50 stream sites with regard to environmental and spatial influences.
3. Cross-product correlations indicated that both factors (spatial and environmental parameters) determined assemblage composition of anurans. Environment itself may be spatially structured, yet this interrelation did not contribute to the explainable variation of frog community compositions within the study area.
4. Detailed analyses of the environmental parameters with nonmetric multidimensional scaling revealed that community structure was mostly affected by three major environmental characters: stream turbidity, river size and the density of understorey vegetation. Based on these habitat characteristics, we assigned species to three distinct habitat guilds.
5. The results underline the importance of riparian habitat heterogeneity in pristine forests in structuring anuran assemblages. We conclude that different anuran assemblages, that is, leaf litter, canopy and stream communities, follow different assemblage rules and thus are not directly comparable.
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 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 30 000 entries lacking start and end annotations in GenBank. Furthermore, 45 000 ITS2 sequences with a questionable annotation were re-annotated. Approximately 30 000 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: 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.
