SBiKF_AG_Janke_Wale Cover ScAdv 2018 April

SBIK-F Arbeitsgruppe

Evolutionäre Genomik

In dieser Arbeitsgruppe vergleichen und untersuchen wir die Genome von Wirbeltieren, mit dem Ziel ihre Evolution besser zu verstehen. Wir konzentrieren uns auf Säugetiere. Sie sind eine ideale Gruppe für solche Studien, da viele Genome verfügbar sind und ständig neue hinzukommen. In bisherigen Studien haben wir unter anderem die Genome verschiedener Giraffen-, Wal- und Bär-Arten sowie Krokodil- und Beuteltier-Arten analysiert.
Einer unserer Schwerpunkte ist die Analyse von Verwandtschaftsbeziehungen zwischen Arten und der (Neu)beschreibung von Stammbäumen anhand von Genomen. Dabei rekonstruieren wir unter anderem den Genfluss zwischen Arten. Unsere bisherigen Forschungsergebnisse hier haben zur Identifikation neuer Giraffenarten geführt und sind damit nicht nur Grundlagenforschung, sondern auch für den Naturschutz relevant. Zudem zeigen unsere Ergebnisse, dass die Entwicklung von Säugetieren – möglicherweise durch Hybridisierungen – wesentlich komplexer verlief, als bisher angenommen wurde. Um diese Komplexität darzustellen, verwenden wir mehrdimensionale Netzwerke.

Ein weiteres Augenmerk unserer Arbeitsgruppe liegt darauf, besser zu verstehen, ob und wie evolutionäre Prozesse der Genome und damit Organismen von Umweltveränderungen gestaltet werden. Die meisten arktischen Wirbeltiere haben sich aus südlichen Artgenossen während des Pleistozäns oder des Holozäns herausbildet und sich daher über relativ kurze Zeiträume an ihre Lebensräume angepasst. Sie sind deshalb eine ideale taxonomische Gruppe zur Studie von genomischen Auswirkungen des Klimawandels.  Dazu suchen wir mit Hilfe moderner genomischer („Next-Generation“) Technologien nach Signaturen im Genom, die auf die Anpassung an das Leben in der Arktis hindeuten.
Um langskalige Veränderungen von Biodiversität und deren Korrelationen mit Umweltveränderungen zu erforschen, nutzen wir zudem Methoden der Bioinformatik. Diese entwickeln wir oder passen sie an, um Säugetiergenome zu studieren. Wenn nötig, produzieren wir eigene Daten um Hypothesen zu testen oder bestehende Genomdaten zu ergänzen.

Links

LOEWE Zentrum für Translationale Biodiversitätsgenomik

Team

Leitung

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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 – Genome structure
Dr. Stefan Prost
PostDoc – Gene flow mammals
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Raphael T. F. Coimbra
Doktorand – 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
Doktorand – 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.

Mitarbeiterfoto
Sven Winter
Doktorand – 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