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:
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.
Publications, Citations, h- and i10-index
Who is Who in Phylogenetic Networks
LOEWE Centre for Translational Biodiversity Genomics
Selected recent publications
Bruno Lopes da Silva Ferrette, Raphael TF Coimbra, Sven Winter, Menno J De Jong, Samuel Mackey Williams, Rui Coelho, Daniela Rosa, Matheus Marcos Rotundo, Freddy Arocha, Bruno Leite Mourato, Fernando Fernandes Mendonça, Axel Janke (2023) Seascape genomics and mitogenomic phylogeography of the sailfish (Istiophorus platypterus) . Genome Biology and Evolution
Menno J de Jong, Aidin Niamir, Magnus Wolf, Andrew C Kitchener, Nicolas Lecomte, Ivan V Seryodkin, Steven R Fain, Snorre B Hagen, Urmas Saarma, Axel Janke (2023) Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence. Communications Biology 6 (1), 153
Magnus Wolf, Menno De Jong, Sverrir Daníel Halldórsson, Úlfur Árnason, Axel Janke (2022) Genomic Impact of Whaling in North Atlantic Fin Whales. Molecular biology and evolution 39 (5)
Raphael TF Coimbra, Sven Winter, Vikas Kumar, Klaus-Peter Koepfli, Rebecca M Gooley, Pavel Dobrynin, Julian Fennessy, Axel Janke (2021) Whole-genome analysis of giraffe supports four distinct species. Current Biology
Stefan Prost, Sven Winter, Jordi De Raad, Raphael TF Coimbra, Magnus Wolf, Maria A Nilsson, Malte Petersen, Deepak K Gupta, Tilman Schell, Fritjof Lammers, Axel Janke (2020) Education in the genomics era: Generating high-quality genome assemblies in university courses. Gigascience
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.
I am interested in the evolution of genomes and genomic diversity in general, including phylogenetic as well as population genetic questions. In my current work, I try to uncover the impact of bottleneck events on the genetic diversity of baleen whales and I would like to understand how depleting population sizes affect these genomes. Therefore, I analyze gene flow and hybridization patterns between whales, but I also aim for new genome publications and phylogenetic insides. With this, I hope to support the conservation and management of whales. Additionally, I worked a lot with genomes of parasitic fungi that possess fast evolving and diverse contents of genes responsible for their pathogenetic behavior, called effectors. In so doing, I tried new machine learning tools that predict these effectors and evaluate their reliability. Eventually, this will speed up our process of finding and analyzing those genes.
10/2019 – present Ph.D. student at the Senckenberg Biodiversity and Climate Research Centre (SBiK-F). Working group of Prof. Dr. Axel Janke
03/2019 – 09/2019 Researcher at Working Group ‘Geobotanics’ at Ruhr-Universität Bochum. Main task: Analysis and publishing of genomic data, tutoring students
10/2016 – 01/2019 Master of Science ‚Biodiversity‘ at Ruhr-Universität Bochum and Universität Duisburg, Essen. Thesis topic: „Genomanalysen des biotrophen Phytoparasiten Urocystis primulicola” supervised by Prof. Dr. Dominik Begerow and PD Dr. Minou Nowrousian
10/2013 – 10/ 2016 Bachelor of Science ‚Biology‘ at Ruhr-Universität Bochum. Thesis topic: „Untersuchung des Flugverhaltens von Sporen der Gattung Urocystis“ supervised by Prof. Dr. Dominik Begerow and Prof. Dr. Ralf Tollrian
I am a postdoctoral researcher studying population genomics and comparative genomics. My main research interest is the question how micro-evolutionary processes translate to speciation and evolutionary innovations. My research focuses particularly on Palearctic mammalian species, including brown bear (Ursus arctos), roe deer (Capreolus capreolus and Capreolus pygargus), and red deer and wapiti (Cervus elaphus, Cervus canadensis and Cervus hanglu).
De Jong et al. 2021, Molecular Ecology Resources,, SambaR: An R package for fast, easy and reproducible population-genetic analyses of biallelic SNP data sets. link
De Jong et al. 2021, Molecular Ecology, Detecting genetic signals of selection in heavily bottlenecked reindeer populations by comparing parallel founder events link
De Jong et al. 2023, Communications Biology, Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence link
I am interested in genomics and population genetics to help future conservation efforts for threatened species, as well as those that aren’t (yet). In addition to that I am also interested in comparative genomics and speciation.
Currently I am working mainly with giraffe genomes and population genetics to further characterize subspecies in Southern Africa. This involves interpopulational gene flow analyses, as well as intrapopulational diversity measures.
2022-present Ph.D. student at the enckenberg Biodiversity and Climate Research Centre (SBiK-F). Working group of Prof. Dr. Axel Janke
10/2019-12/2021 Master of Science „Ecology and Evolution“ at Goethe University Frankfurt. Thesis topic: „Long-read based de novo genome assembly and analyses of a hybrid turtle genome (Geoemydidae)“ supervised by Prof. Dr. Axel Janke and Prof. Dr. Uwe Fritz
10/2016-10/2019 Bachelor of Science „Biosciences“ at Goethe University Frankfurt. Thesis topic: „Airborne fungal spores above the Amazon rainforest“ supervised by Prof. Dr. Piepenbring and Dr. Ralph Mangelsdorff
Sven Winter et al. Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra, Gigabyte,1,2020 https://doi.org/10.46471/gigabyte.6
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.
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
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