Young Research Group

Transposable Elements

Our research focus is on the dynamics and evolution of transposable elements as well as phylogenomic reconstruction.

Transposable elements (TEs) are typically 300 to 6,000 nucleotides long sequences that occur in multiple copies and make up 40-50% of mammalian genomes. They are present in all eukaryotes. Unlike genes, TEs move around in the genome (“jumping genes”).

TEs are evolving in an intricate balance with their host genome and the interchange between different transposable elements within the host genome can therefore be seen as a genomic ecosystem. As in natural ecosystems, introduction or extinction of transposable elements can have dramatic long-term effects on the genome. These can include diseases, morphological changes, and adaptations. As such, transposable elements have become a popular research field because of their potential implications in medical research. Currently, more than 1,500 different types of TEs are known from the human genome alone. However, the genomes of other species are currently ‘black boxes’ and the role and implication of TE’s in these genomes is largely unknown.  My research group therefore focusses on recently developed tools to screen genomes for known and novel TEs. This will allow us to understand lineage-specific differences in TE composition on a comparative scale, and additionally will give insights in horizontal and vertical transmissions of TEs.

Phylogenomic reconstruction: Compared to using single loci to reconstruct evolutionary histories, analysis of the complete genome allows a much finer scaled picture. Genome sequences harbor signals of past evolutionary events such as bottlenecks and introgression and effective population sizes. This helps to reconstruct the complete picture of the evolution of species.

Current research projects

Several projects are ongoing ranging from mammals and birds to crabs. We currently aim to understand the evolutionary diversification of a Palearctic specialist bird, the nutcracker (Nucifraga caryocatactes). The nutcracker project include collaborations with SBiK-F (Neuschulz, Schleuning), Senckenberg Dresden (Päckert), as well as NRM, Stockholm.

Recent publications

Lammers F, Blumer M, Rücklé C, Nilsson MA. (2019): Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation. Mob DNA. 10:5.

Nilsson MA, Zheng Y, Kumar V, Phillips MJ, Janke A. (2018): Speciation generates mosaic genomes in kangaroos. Genome Biol Evol, . 10:33-44

Lammers F, Gallus S, Janke A, Nilsson MA. (2017): Phylogenetic conflict in bears identified by automated discovery of transposable element insertions in low-coverage genomes.  Genome Biol Evol . 9:2862-2878.

Gallus, S, Hallström, BM, Kumar, V, Dodt, WG, Janke, A, Schumann GG, Nilsson MA. (2015): Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. Mol Biol Evol. 32(5):1268-83

Team

Head

Mitarbeiterfoto
Dr. Maria Nilsson-Janke
Researcher, Head of Young Research Group 'Transposable Elements'

Research interests

My research focus is on the dynamics of mobile genetic elements, in particular transposable elements in mammalian genomes.
 
What is a transposable element?
Transposable elements (TEs) are typically 300 to 6000 nucleotides long sequences that occur in multiple copies and make up 40-50% of the mammalian genome. They are present in all eukaryotes. TEs are divided into two classes, the retrotransposons and the DNA transposons. Common to the two classes is their ability to move around in the genome (“jumping genes”). Retrotransposons use a ‘copy-and-paste’ approach of an RNA intermediate and can thus multiply a million-fold by “pasting” new copies into the genome in a short time frame. To date there is no biochemical removal mechanism described. Therefore, every new copy in a genome will remain as a silent fossil, as an evidence for an integration event.
 
Transposable elements as unique relationship markers
TEs in the genome are inherited to all descendants and are thus an ideal marker system to resolve evolutionary questions. The genetic properties of TE inheritance make it a marker system that is independent from morphological or sequence analyses and offers a third way to resolve the phylogenetic history. The strength of TEs as evolutionary markers is that they are not affected by adaption such as morphological characters, and have virtually unlimited character states compared to traditional sequence analysis.
  
The ‘biodiversity’ of TEs in mammalian genomes
More than 500 different types of TEs, are known from the human genome. They are evolving in an intricate balance with the host genome. The interchange between different transposable elements within the host genome can be seen as a genomic ecosystem. As in natural ecosystems, introduction or extinction of transposable elements can have dramatic long-term effects on the genome, among others: causing disease, morphological changes, and adaptations.
The human genome and its transposable elements are being studied in detail, because of the medical implications. However, the genomes of other mammalian genomes are currently ‘black boxes’. Therefore, we study the impact of transposable elements on genome structure and composition in several distantly related mammalian groups.

2011- Post Doc Senckenberg
2010 Post Doc Lund University, Sweden
2007-2009 Post Doc Muenster University, Germany
2001-2006 PhD Lund University, Sweden

Selected recent publications:

Nilsson, MA. (2015) The devil is in the details: transposable element analysis of the Tasmanian devil genome. Mobile Genetic Elements. Gene

Gallus, S, Kumar, V, Bertelsen, MF, Janke, A, Nilsson, MA. (2015) A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla). Gene, 571(2):271-8.

Gallus, S, Kumar, V, Janke, A, Nilsson, MA. (2015) Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses. Genome Biol Evol. 7(4):985-92

 

Publications

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

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.