Center for Computational and Theoretical Biology

Molecular Biodiversity Research

Our research projects focus on a combination of field ecology with bioinformatics and new sequencing technologies. Conceptually, we are interested in patterns and structuring forces of communities, where organisms are not easily identifiable or distinguishable from each other. This interest applies to various levels, starting with abundance and diversity of taxa, over phylogenetic reconstructions, towards environmental and spatial influences and lastly regarding organisms' molecular interactions with each other on a genomic level. Methodologically, the workgroup is developing computational workflows and databases as well as laboratory protocols to analyse ecological samples with next-generation sequencing technologies. 

Biologically, the focus of current projects is the dynamics of bacteria-host associations in changing environments. Regarding this, we currently consider changes in microbiota induced by 

  • symbiotic host-host interactions,
  • the host's development,
  • geographic intra-specific variability,
  • climatic changes,
  • prey capturing,
  • as well as general variation between tissues and species of hosts. 

To answer these questions, we conduct field work, analyse samples in our molecular laboratory and apply computational approaches. We have successfully developed methods to simultaneously assess biodiversity of bacteria and plants (here: mixed pollen samples) through next-generation sequencing allowing a very fine scaled interpretation of plant-bee-microbe interactions. Usually we start with descriptive studies, investigating the status-quo, which are followed by experimental designs manipulating the associations by (e.g. antibiotic) exclusion and bioassays. Lastly, for prospective bacteria with interesting distributions and activity, we are also engaged into genomics, studying the genetic possibilities that bacteria bring into the associations with their respective hosts.


[ 2017 ] [ 2016 ] [ 2015 ] [ 2014 ] [ 2013 ] [ 2011 ] [ 2010 ] [ 2009 ] [ 2008 ]

2017 [ nach oben ]

  • Release from prey preservation behavior via prey switch allowed diversification of cuticular hydrocarbon profiles in digger wasps. Wurdack, Mareike; Polidori, Carlo; Keller, Alexander; Feldhaar, Heike; Schmitt, Thomas in Evolution (2017). in press
  • Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen. Danner, Nadja; Keller, Alexander; Härtel, Stephan; Steffan-Dewenter, Ingolf in PLoS one (2017). in press
  • Generalist social bees maximize diversity intake in plant species-rich and resource-abundant environments. Kaluza, Benjamin F.; Wallace, Helen; Keller, Alexander; Heard, Tim A.; Jeffers, Bradley; Drescher, Nora; Blüthgen, Nico; Leonhardt, Sara D. in Ecosphere (2017). 8(3) e01758--n/a.

2016 [ nach oben ]

  • TBro: visualization and management of de novo transcriptomes. Ankenbrand, Markus J.; Weber, Lorenz; Becker, Dirk; Förster, Frank; Bemm, Felix in Database (2016). 2016
  • Silent listeners: Can preferences of eavesdropping midges predict the parasitism risk of their host? Meuche, Ivonne; Keller, Alexander; Ahmadsah, Hanyrol; Ahmad, Norhayati; Grafe, T Ulmar in Behavioral Ecology (2016). 27 995-1003.
  • Pollen DNA barcoding: current applications and future prospects. Bell, Karen; De Vere, Natasha; Keller, Alexander; Richardson, Rodney; Gous, Annemarie; Burgess, Kevin; Brosi, Berry in Genome (2016). 59 629-640.
  • Laboratory rearing of solitary bees and wasps. Becker, Mira; Keller, Alexander in Insect Science (2016). 23 918.
  • Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1. Horn, Hannes; Keller, Alexander; Hildebrandt, Ulrich; Kämpfer, Peter; Riederer, Markus; Hentschel, Ute in Standards in Genomic Sciences (2016).
  • DNA-Metabarcoding – ein neuer Blick auf organismische Diversität. Keller, Alexander; Grimmer, Gudrun; Sickel, Wiebke; Ankenbrand, Markus J in BioSpektrum (2016). 22 147-150.
  • Crown galls of grapevine (Vitis vinifera) host distinct microbiota. Faist, Hanna; Keller, Alexander; Hentschel, Ute; Deeken, Rosalia in Applied and Environmental Microbiology (2016). 82 5542-5552.
  • Contact of myeloma cells induces a characteristic transcriptome signature in skeletal precursor cells--Implications for myeloma bone disease. Dotterweich, Julia; Schlegelmilch, Katrin; Keller, Alexander; Geyer, Beate; Schneider, Doris; Zeck, Sabine; Tower, Robert JJ; Ebert, Regina; Jakob, Franz; Schütze, Norbert in Bone (2016). 93 155--166.
  • biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format. Ankenbrand, Markus J.; Terhoeven, Niklas; Hohlfeld, Sonja; Förster, Frank; Keller, Alexander in F1000Research (2016). 5 2348.
  • bcgTree: automatized phylogenetic tree building from bacterial core genomes. Ankenbrand, Markus J; Keller, Alexander in Genome (2016). 59 783-791.
  • Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies. Sickel, Wiebke; Grafe, T. Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander in Microbial Ecology (2016). 71 938–953.

2015 [ nach oben ]

  • Reptiles as reservoirs of bacterial infections: real threat or methodological bias? Zancolli, Giulia; Mahsberg, Dieter; Sickel, Wiebke; Keller, Alexander in Microbial Ecology (2015). 70(3) 579-84.
  • Monophyletic clades of Macaranga pollinating thrips with high specificity to host plant taxonomic sections. Fiala, Brigitte; Wells, Konstans; Haubenreisser, Julia; Pittroff, Andreas; Kaya-Zeeb, Sinan; Chung, Arthur Y.C.; bin Hashim, Rosli; Keller, Alexander in Biological Journal of the Linnean Society (2015). 116(3) 558–570.
  • Microhabitat heterogeneity across leaves and flower organs promotes bacterial diversity. Junker, Robert R; Keller, Alexander in FEMS Microbiology Ecology (2015). 91(1) fiv09.
  • ITS2 Database V: Twice as Much. Ankenbrand, Markus J.; Keller, Alexander; Wolf, Matthias; Schultz, Jörg; Förster, Frank in Molecular Biology and Evolution (2015). 32(11) 3030-3032.
  • Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach. Sickel, Wiebke; Ankenbrand, Markus; Grimmer, Gudrun; Holzschuh, Andrea; Härtel, Stephan; Lanzen, Jonathan; Steffan-Dewenter, Ingolf; Keller, Alexander in BMC Ecology (2015). 15 20.
  • Functional and phylogenetic diversities of plant communities differently affect the structure of flower-visitor interactions and reveal convergences in floral traits. Junker, Robert R.; Blüthgen, Nico; Keller, Alexander in Evolutionary Ecology (2015). 29 437-450.
  • Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples. Keller, Alexander; Danner, Nadja; Grimmer, Gudrun; Ankenbrand, Markus; von der Ohe, Katharina; von der Ohe, Werner; Rost, Simone; Härtel, Stephan; Steffan-Dewenter, Ingolf in Plant Biology (2015). 17 558-566.
  • DNA-analyses of Venerupis philippinarum (Adams and Reeve, 1850) with a new and constant shell-pattern from Italy, Emilia Romagna. Wölfling, Mirko; Rohrhirsch, Manuela; Uhl, Britta; Keller, Alexander in Malacologia (2015). 86(1) 30-32.

2014 [ nach oben ]

  • Pollen DNA barcoding using next-generation sequencing. Keller, Alexander; Härtel, Stephan; Steffan-Dewenter, Ingolf in Barcode Bulletin (2014). 5(3) 8.
  • Identification of WISP1 as an important survival factor in human mesenchymal stem cells. Schlegelmilch, Katrin; Keller, Alexander; Zehe, Viola; Hondke, Silvia; Klein-Hitpass, Ludger; Schütze, Norbert in Gene (2014). 551(2) 243-54.
  • Density-dependent responses by bumblebees to flower dwelling bacteria. Junker, Robert R; Romeike, Tanja; Keller, Alexander; Langen, Daniela in Apidologie (2014). 45 467-477.
  • Confirmation of warfarin resistance of naturally occurring VKORC1 variants by coexpression with coagulation factor IX and in silico protein modelling. Müller, Elisabeth; Keller, Alexander; Fregin, Andreas; Müller, Clemens R; Rost, Simone in BMC Genetics (2014). 15 17.

2013 [ nach oben ]

  • Only distance matters--non-choosy females in a poison frog population. Meuche, Ivonne; Brusa, Oscar; Linsenmair, K Eduard; Keller, Alexander; Pröhl, Heike in Frontiers in Zoology (2013). 10(1) 29.
  • Diverse microbiota identified in whole intact nest chambers of the red mason bee Osmia bicornis (Linnaeus 1758). Keller, Alexander; Grimmer, Gudrun; Steffan-Dewenter, Ingolf in PloS one (2013). 8(10) e78296.

2011 [ nach oben ]

  • Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. Buchheim, Mark A; Keller, Alexander; Koetschan, Christian; Förster, Frank; Merget, Benjamin; Wolf, Matthias in PLoS One (2011). 6(2) e16931.
  • Composition of epiphytic bacterial communities differs on petals and leaves. Junker, Robert R; Loewel, Christina; Gross, Roy; Dötterl, Stefan; Keller, Alexander; Blüthgen, Nico in Plant Biology (2011). 13(6) 918--924.

2010 [ nach oben ]

  • The ITS2 Database III—sequences and structures for phylogeny. Koetschan, Christian; Förster, Frank; Keller, Alexander; Schleicher, Tina; Ruderisch, Benjamin; Schwarz, Roland; Müller, Tobias; Wolf, Matthias; Schultz, Jörg in Nucleic Acids Research (2010). 38(Suppl 1) D275--D279.
  • Ribosomal RNA phylogenetics: the third dimension. Keller, Alexander; Wolf, Matthias; Dandekar, Thomas in Biologia (2010). 65(3) 388--391.
  • ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to em Coelastrum em (Chlorophyta, Chlorophyceae), including the new genera em Comasiella em and em Pectinodesmusem. Hegewald, Eberhard; Wolf, Matthias; Keller, Alexander; Friedl, Thomas; Krienitz, Lothar in Phycologia (2010). 49(4) 325--335.
  • Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Keller, Alexander; Förster, Frank; Müller, Tobias; Dandekar, Thomas; Schultz, Jörg; Wolf, Matthias; others, in Biology Direct (2010). 5 4.

2009 [ nach oben ]

  • The importance of environmental heterogeneity for species diversity and assemblage structure in Bornean stream frogs. Keller, Alexander; Rödel, Mark-Oliver; Linsenmair, K Eduard; Grafe, T Ulmar in Journal of Animal Ecology (2009). 78(2) 305--314.
  • ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus em Agrodiaetus em (Lepidoptera: Lycaenidae: \em Polyommatus\em ). Wiemers, Martin; Keller, Alexander; Wolf, Matthias in BMC Evolutionary Biology (2009). 9(1) 300.
  • Die Artenvielfalt der Amphibien in einem Tieflandregenwald auf Borneo. Keller, Alexander (2009). 80--83.
  • A Bornean amphibian hotspot: the lowland mixed dipterocarp rainforest at Ulu Temburong National Park, Brunei Darussalam. Grafe, T Ulmar; Keller, Alexander in Salamandra (2009). 45 16--25.
  • 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Keller, Alexander; Schleicher, Tina; Schultz, Jörg; Müller, Tobias; Dandekar, Thomas; Wolf, Matthias in Gene (2009). 430(1) 50--57.

2008 [ nach oben ]

  • ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). Keller, Alexander; Schleicher, Tina; Förster, Frank; Ruderisch, Benjamin; Dandekar, Thomas; Müller, Tobias; Wolf, Matthias in BMC Evolutionary Biology (2008). 8(1) 218.
  • Geographic distribution: Xenodermus javanicus (Short Note). Keller, Alexander; Siegle, Matthias; Grafe, T Ulmar in Herpetological Review (2008). 39 373.
  • Geographic distribution: Parias sumatranus (Short Note). Keller, Alexander; Siegle, Matthias; Grafe, T Ulmar in Herpetological Review (2008). 39 373.