Research Group

Evolutionary Vertebrate Genomics

Our research group compares and analyzes the genomes of vertebrates to get a better understanding of their evolution. We focus on mammals. Mammals are particularly suitable for such research because many mammal genomes are already available and new ones are being sequenced constantly. In previous studies we have looked into the genomes of giraffe, whale and bear species as well as crocodile and marsupial species.

To address our primary research question we analyze relationships between species and (re)build phylogenetic trees based on genomes. In doing this we reconstruct gene flow between species. Our research in this field has shown that there are more giraffe species that were previously acknowledged and basic research results can be relevant for conservation efforts. Furthermore our studies show that the evolution of mammals has been a lot more complex than previously thought, probably including hybridization. To visualize this process, we use multi-dimensional networks.
Next to this, our research group looks into the question how environmental processes shape the evolution of genomes, and consequently organisms. Most arctic vertebrates diverged from southern species during the Pleistocene or Holocene, i.e. they have adapted to arctic conditions over relatively short time frames. Therefore they are an ideal taxonomic group to study genomic effects of climate changes. To investigate the genomic effects and signatures of adaptation to life in the arctic, we use modern (”next-generation”) genomic techniques.

In order to study long-scale changes in biodiversity and their correlation with environmental changes, we also make use of bioinformatics tools. We develop or adapt them to our questions in order to analyze mammalian genome sequences. When necessary we will produce new sequence data to test hypothesis testing and complement existing data.

Links

Selected publications

Arnason, U., Lammers, F., Kumar, V., Nilsson, M.A. Janke A (2018) Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. Science Advances, doi: 10.1126/sciadv.aap9873

Kumar, V., Lammers, F., Bidon, T., Pfenninger, M., Kolter, L., Nilsson, M.A. and Janke, A. (2017) The evolutionary history of bears is characterized by gene flow across species. Scientific Reports, doi: 10.1038/srep46487

Fennessy, J., Bidon, T., Reuss, F., Kumar, V., Elkan, P., Nilsson, M.A., Vamberger, M., Fritz, U. and Janke, A. (2016) Multi-locus analyses reveal four giraffe species instead of one. Current Biology, doi: 10.1016/j.cub.2016.07.036

Team

Head

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Prof. Dr. Axel Janke
Professor, Head of Research Group 'Evolutionary vertebrate genomics'

CV

I am interested in the evolution of vertebrates in general, including marsupials, birds, almost every placental mammalian order, lizards, snakes, crocodiles and fishes. Besides reconstructing and dating their evolutionary tree, placing the events into larger contexts of e.g. biogeography, plate tectonics and climate is exciting. The increasing amount of genomic data show that evolution may not be a bifurcating process, but seeing it as a network will enhance our understanding of evolution. Currently – as of January 2017 – I am interested and working on the following topics for which PhD, master or project students are welcome:
Giraffe Research  
Mammalian phylogenomics (see D2.3)
Arctic adaptation (see D2.4)
Genomics and speciation (see D2.3)
Genomics and climate (environmental) change (see D2.4)
The basic divergences of crocodiles
The evolution of marsupials
Click here for more information about the topics.

External links

Publications, Citations, h- and i10-index
Who is Who in Phylogenetic Networks

LOEWE Centre for Translational Biodiversity Genomics

Selected recent publications

Arnason,  U., Lammers, F., Kumar, V., Nilsson, M.A. Janke A (2018) Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. Science Advances

Kumar, V., Lammers, F., Bidon, T., Pfenninger, M., Kolter, L., Nilsson, M.A. and Janke, A. (2017) The 
evolutionary history of bears is characterized by gene flow across species. Scientific Reports 

Fennessy, J., Bidon, T., Reuss, F., Kumar, V., Elkan, P., Nilsson, M.A., Vamberger, M., Fritz, U. and Janke, A. (2016) Multi-locus analyses reveal four giraffe species instead of one. Current Biology

Bidon, T., Schreck, N., Hailer, F., Nilsson, M.A., Janke A (2015) Genome-wide search identifies 1.9 megabases from the polar bear Y chromosome for evolutionary analyses. Genome Biol Evol

Gallus, S., Hallström, B.M., Kumar, V., Janke, A., Ning, Z., Murchison, E.M., Yang, F., Fu, B., Bertelsen, M.F., Schumann, G.G., Nilsson, M.A. (2015) Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. Mol Biol Evol (early access)

Kutschera, V. E., Bidon, T., Hailer, F., Rodi, J. L., Fain, S. R., Janke, A. (2014) Bears in a forest of gene trees: Phylogenetic inference is complicated by incomplete lineage sorting and gene flow. Molecular Biology and Evolution, MBE2014/06/05/molbev.msu186

Bapteste, E., van Iersel, L., Janke, A., Kelchner, S., Kelk, S., McInerney, J. O., Morrison, D. A., Nakhleh, L., Steel, M., Stougie, L., Whitfield, J. (2013) Networks: expanding evolutionary thinking. Trends in Genetics 29:439-441. doi: 10.1016/j.tig.2013.05.007.

Arnason,  U., Lammers, F., Kumar, V., Nilsson, M.A. Janke A (2018): Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow. Science Advances.

Dr. Vladimir Kapitonov
PostDoc, Member of Research Group 'Evolutionary vertebrate genomics'
PostDoc – Genome structure
Dr. Stefan Prost
Postdoc, Member of Research Group 'Evolutionary vertebrate genomics'
PostDoc – Gene flow mammals
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Raphael T. F. Coimbra
Ph.D. Student, Member of Research Group 'Evolutionary vertebrate genomics'
Phd student – Giraffe genomics

Research interests

I am interested in evolutionary biology in general, but mostly in biogeography, phylogeography and phylogenetics. I am also enthusiastic about learning new genome sequencing techniques and bioinformatics to understand evolution based on large-scale genomic data. Currently, I am working on evolutionary genomics and population genetics of giraffes. The aim is to investigate hybridization and gene flow between four putative giraffe species using next generation sequencing data in order to verify the current taxonomic proposal and to understand their speciation process. For my B.Sc. and M.Sc. studies, I have worked on the phylogeography and conservation genetics of xenarthran species, mainly anteaters and sloths.

2018 – present Ph.D. student at the Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany. Working group of Prof. Dr. Axel Janke.

2015 – 2017 M.Sc. in Genetics with emphasis in Evolutionary and Population Genetics at the Universidade Federal de Minas Gerais (UFMG), Brazil. Thesis: “Genetic structure, population dynamics and historical demography of the giant anteater Myrmecophaga tridactyla Linnaeus, 1758 (Pilosa: Myrmecophagidae)”. Supervised by Prof. Dr. Fabrício Rodrigues dos Santos.

2010 – 2015 B.Sc. in Biological Sciences at the Universidade Federal de Minas Gerais (UFMG), Brazil. Thesis: “Estrutura genética populacional do tamanduaí (Cyclopes didactylus)” [Population genetic structure of the silky anteater (Cyclopes didactylus)]. Supervised by Prof. Dr. Fabrício Rodrigues dos Santos.

Coimbra R.T.F., Miranda F.R., Clozato C.L., Schetino M.A.A., Santos F.R. (2017) Phylogeographic history of South American populations of the silky anteater Cyclopes didactylus (Pilosa: Cyclopedidae). Genetics and Molecular Biology 

Jordi de Raad
Ph.D. student, Member of Research Group 'Evolutionary vertebrate genomics' and Young Research Group 'Transposable Elements'
PhD student – Bird genomics

Research Interests

As a molecular ecologist, I have always been amazed by the rapid-evolving fields of genomics and genetics and its underlying potential. I am mainly interested in applying genomic and genetic methods to elucidate evolutionary uncertainties and to contribute to the conservation of our biodiversity.  During my Msc thesis, I have worked on the genetics of the endangered Eurasian Black Vulture, resulting in a general interest in the (highly conserved) genome of birds. Currently, I am working on evolutionary genomics and geneticsin passerine birds. The aim is to resolve phylogenies, examine evolutionaryhistories and to link this data with varying ecological and morphologicaltraits.

Short CV

2018 – present Ph.D. student at the Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany. Working group of Prof. Dr. Axel Janke

2015 – 2017 Msc Environmental Biology at the University of Utrecht, the Netherlands. Thesis topic: “First insights in the reintroduction of the Eurasian Black Vulture (Aegypius monachus) in Southern-France – evaluating individual contribution, genetic diversity and population genetic structure”. Supervised by dr. Peter Galbusera and Philippe Helsen

2014 – 2015 Student assistant at the department of Biology and Biomedical Sciences at the University of Utrecht, the Netherlands.

2009 – 2013 Bsc Biology at the University of Utrecht, the Netherlands.

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Sven Winter
Ph.D. Student, Member of Research Group 'Evolutionary vertebrate genomics'
PhD student – Giraffe gene flow

Research Interests

I am interested in evolutionary biology and taxonomy of mammals. Since visiting Namibia for my Bachelor thesis I am fascinated of large African mammals. Currently, my research focuses on evolutionary genomics and population genetics of giraffe (Giraffa carmelopardalis). The aim is to identify structure and gene flow of wild giraffe populations based on mitochondrial and nuclear markers in order to examine the need for a taxonomic revision in giraffes.

CV
Since 2016 PhD student at Biodiversity and Climate Reasearch Centre (BiK-F), Frankfurt am Main, Germany
Working group of Prof. Dr. Axel Janke
2016 Master of Science (Zoology) at University of Vienna, Austria.
Master thesis: “A molecular phylogeny and divergence times of the weevil tribe Apionini (Brentidae, Curculionoidea, Coleoptera”, Supervisor: Prof. Dr. Konrad Fiedler
2014 – 2016 Studies of biology at University of Vienna, Austria
Master degree course: Zoology
2013 Bachelor of Science at Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
Bachelor thesis: “Beutespektren namibischer Prädatoren mit Schwerpunkt auf dem Leopard Panthera pardus auf Farmland in Namibia” (Prey spectra of namibian predators with focus on leopard Panthera pardus on Farmland in Namibia), Supervisor: Dr. Renate van den Elzen
2010 – 2013 Studies of biology at Rheinische Friedrich-Wilhelms-Universität Bonn, Germany. Bachelor degree course: Biology

Andrea Kolb
Administrative coordination of Research Group 'Molecular ecology' and 'Evolutionary vertebrate genomics'