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tRNA evolution

Front cover PhD thesis Peter van der Gulik

Transfer RNAs (tRNA) are an integral component of translation in the three domains of life (Archaea, Bacteria and Eukaryotes). In this project, we are searching for domain-specific patterns in the set of tRNAs that are used.

We are also investigating whether these patterns can help assess the completeness of newly assembled genome sequences.

Collaborators:

Black Rhinoceros genome

The “Rhinoceromics” project at the Leiden Centre for Applied Bioscience is studying health issues in captive black rhino’s using various omics techniques, including metagenomics. As a sideline, we wanted to see whether we could assemble a large eukaryotic genome using only nanopore reads. This produced an assembly of comparable size and contiguity to the current reference genome for this species. Our assembly will be used as reference assembly in the metagenomics project.

Dré Kampfraath

co-supervised with Jacintha Ellers at the Vrije Universiteit Amsterdam

In his PhD work, Dré is using comparative genomics to study the loss of traits due to interactions between the springtail Folsomia candida and bacteria Wolbachia pipientis. This springtail has become dependent on Wolbachia for its reproduction. Using a combination of lab-experiments and genomics he searches for the phenotypic and genotypic loss of traits that led to this obligate relationship.

Mark Lammers

co-supervised with Jacintha Ellers at the Vrije Universiteit Amsterdam

* Mark defended his thesis on 30 sept 2020

I am an integrative biologist, interested in all aspects of the evolutionary ecology of the mega-diverse insects. My research is primarily question-driven. To test the ensuing wide range of hypotheses, I apply a diverse set of methods and theory. These derive from several major fields of biology:

  • Evolutionary biology: Physiological and local adaptation, molecular evolution, life-history evolution, niche differentiation, speciation, phenotypic plasticity;
  • Entomology: Behaviour, ecology, and evolution of insects, particularly parasitoid wasps;
  • Bioinformatics: Transcriptomics, comparative genomics, data analysis and statistics, custom pipelines in R and bash (Linux).

My PhD research was on physiological adaptation at the Vrije Universiteit Amsterdam with Jacintha Ellers and Ken Kraaijeveld, where I wrote my thesis with the title ‘The evolutionary loss of lipogenesis in insect parasitoids: Molecular mechanisms and ecological aspects’. In this work, I unravelled the gene regulatory mechanisms that inhibit lipogenesis while maintaining the underlying genes’ pleiotropic functions in the model species Nasonia vitripennis (Hymenoptera: Pteromalidae).

Currently I work as a junior group leader (“Wissenschaftlicher Mitarbeiter”) with Jürgen Gadau in Münster. There I work on five main projects on evolutionary processes that may contribute to the vast biodiversity of insect parasitoids:

  • Rapid adaptation to novel hosts;
  • Evolutionary transitions and the loss of sexual reproduction;
  • Genome evolution of parasitoids with peculiar lifestyles;
  • Pre-zygotic reproductive isolation in (contemporary) parasitoid speciation;
  • Chemical ecology of courtship behaviour in the parasitoid Aphidius ervi.

marklammers.nl

Jens Bast

cosupervised with Stefan Scheu at Georg-August University Gottingen, Germany

*Jens obtained his PhD “summa cum laude” on 30 January 2015

I am interested in the evolution of reproductive systems. My PhD thesis (in the Scheu group at the University of Goettingen, co-supervised by Ken Kraaijeveld) focused on transposable elements (TEs) as deleterious agents driving mutational meltdown in asexual lineages. Contradictory to non-recombining regions within sexual genomes, such as Y-chromosomes, asexuals do not harbor increased TE loads compared to sexual sister taxa. This suggests fundamentally different forces acting on completely linked asexual genomes compared to non-recombining regions and hints at TE self-regulation in these animals.
Current research (in the Schwander group at the University of Lausanne) comprises elucidating consequences of asexual reproduction in Timema stick insects and oribatid mites (in collaboration with the Scheu group), such as identifying deleterious mutations and counteracting forces (including TEs and gene conversion), consequences of long-term asexuality (allelic sequence divergence), and mechanisms of evolutionary innovation (horizontal gene transfer and structural rearrangements).
Further, I am interested in the  differences of mito-nuclear interactions in sexual and asexual animals, as well as the role of ecological factors (such as resources) as explanatory forces for the maintenance of sex (i.e. high recombination rates in most animals).

Jens has recently started his own lab at the University of Cologne
www.jensbast.com