Phylogenetics

Research Interests (Wolf Lab - RNA sequence-structure phylogenetics)

Abstract: Our research in evolutionary biology and in the systematics of animals and plants focuses on the meeting points of phylogenetics and bioinformatics. Further keywords are molecular systematics, biodiversity, morphology, and taxonomy, as well as biophilosophy (species concepts) and science education. Focusing on alignments and rRNA secondary structures, in particular of the 18S and the internal transcribed spacer 2 (ITS2), as well as on co-developing computer tools inferring RNA sequence-structure phylogenies, we are mainly interested in the phylogenetic relationships and the evolution of protists (protozoa and algae - in particular of alveolates, Euglenozoa, green algae, and stramenopiles), and of invertebrate Metazoa. However, we are working on phylogenetic relationships throughout the tree of life, i.e., on the phylogeny and the evolution of prokaryotes, protists, and Metazoa, as well as on the phylogeny and the evolution of Fungi and 'higher' plants, always connecting organismal- with molecular biology, as well as lab- and field work with computational biology. Our main achievement is the development of the ITS2 database and related software (e.g. 4SALE and ProfDistS). In the context of our phylogenetic RNA sequence-structure analyses, our tools (for alignment and tree reconstruction) are able to automatically process RNA sequences and their individual secondary structures simultaneously.

Key words: algae; 18S; ITS2; internal transcribed spacer 2; phylogeny; RNA; secondary structure; ITS2 database; 4SALE; ProfDistS.

Selected Publications (Bioinformatics)

ITS2 database V: Twice as much.
Markus J Ankenbrand, Alexander Keller, Matthias Wolf, Jörg Schultz, Frank Förster
(2015) Molecular Biology and Evolution 32:3030–3032.

ITS2, 18S, 16S or any other RNA - simply aligning sequences and their individual secondary structures simultaneously by an automatic approach.
Matthias Wolf, Christian Koetschan, Tobias Müller
(2014) Gene 546:145-149.

5.8S-28S rRNA interaction and HMM-based ITS2 annotation.
Alexander Keller, Tina Schleicher, Jörg Schultz, Tobias Müller, Thomas Dandekar, Matthias Wolf
(2009) Gene 430:50-57.

ProfDistS: (Profile-) Distance based phylogeny on sequence - structure alignments.
Matthias Wolf, Benjamin Ruderisch, Thomas Dandekar, Jörg Schultz, Tobias Müller
(2008) Bioinformatics 24:2403-2404.

4SALE - a tool for synchronous RNA sequence and secondary structure alignment and editing.
Philipp N Seibel, Tobias Müller, Thomas Dandekar, Jörg Schultz, Matthias Wolf
(2006) BMC Bioinformatics 7:11.

Selected Publications (Phylogeny)

18S rDNA sequence-structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida).
Antonia S Rackevei, Anna Karnkowska, Matthias Wolf
(2023) Journal of Eukaryotic Microbiology 70:e12959.

Paramecium: RNA sequence-structure phylogenetics.
Marlyn Weimer, Peter Vďačný, Matthias Wolf
(2023) International Journal of Systematic and Evolutionary Microbiology 73:5744.

18S rRNA gene sequence-structure phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with special reference to Trypanosoma.
Alyssa Borges, Markus Engstler, Matthias Wolf
(2021) European Journal of Protistology 81:125824.

Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota).
Christian Koetschan, Sandra Kittelmann, Jingli Lu, Djamila Al-Halbouni, Graeme N. Jarvis, Tobias Müller, Matthias Wolf, Peter H. Janssen
(2014) PLoS One 9:e91928.

Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data.
Matthias Wolf, Tobias Müller, Thomas Dandekar, J Dennis Pollack
(2004) International Journal of Systematic and Evolutionary Microbiology 54:871-875.

Selected Publications (Phycology)

ITS2 and 18S rDNA sequence-structure phylogeny of Chlorella and allies (Chlorophyta, Trebouxiophyceae, Chlorellaceae).
Jaqueline S Heeg, Matthias Wolf
(2015) Plant Gene 4:20-28.

'Y'Scenedesmus (Chlorophyta, Chlorophyceae): the internal transcribed spacer 2 rRNA secondary structure re-revisited.
Sebastian M Markert, Tobias Müller, Christian Koetschan, Thomas Friedl, Matthias Wolf
(2012) Plant Biology 14:987-996.

Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life.
Mark A Buchheim, Alexander Keller, Christian Koetschan, Frank Förster, Benjamin Merget, Matthias Wolf
(2011) PLoS One 6:e16931.

Microevolution and Speciation in Thalassiosira weissflogii (Bacillariophyta).
Ulf Sorhannus, Joseph D Ortiz, Matthias Wolf, Martin G Fox
(2010) Protist 161:237-249.

Phylogenetic relationship of Chlorella and Parachlorella gen. nov. (Chlorophyta, Trebouxiophyceae).
Lothar Krienitz, Eberhard H Hegewald, Dominik Hepperle, Volker AR Huss, Thomas Rohr, Matthias Wolf
(2004) Phycologia 43:529-542.