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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.


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

In my PhD project, I attempt to elucidate the molecular mechanisms behind the evolutionary loss of lipogenesis in parasitoids. This requires a healthy mix of wet-lab molecular analyses, bio-informatics and experiments with live insects.

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

Barbara Reumer

cosupervised with Jacques van Alphen at Leiden University, The Netherlands

*Barbara defended her thesis on 30 May 2012*

For my PhD-project, I am studying parthenogenesis-inducing Wolbachia bacteria in two parasitoid wasps, Tetrastichus coeruleus and Asobara japonica.
Wolbachia are intracellular, symbiotic bacteria belonging to the order Rickettsiales within the a-Proteobacteria. Wolbachia is known to infect a wide range of arthropods, including insects, spiders, mites, scorpions and isopods, and has also been found in nematodes. A recent analysis estimated that 66% of all insect species is infected with Wolbachia. Wolbachia is maternally inherited, since a sperm cell contains too little cytoplasm to harbour the bacterium. Therefore, they benefit from female-biased sex ratios in their hosts. To enhance its own transmission to the next generation, Wolbachia can induce various alterations of the reproduction mechanism of its host, such as cytoplasmic incompatibility, feminization, male killing and parthenogenesis. Wolbachia-induced parthenogenesis is most commonly found in haplodiploid organisms, such as Hymenoptera.
Tetrastichus coeruleus (Hymenoptera) is an egg-larval parasitoid of the Asparagus beetle (Crioceris asparagi). C. asparagi lives on the Asparagus plant (Asparagus officinalis), which grows on sandy soils, such as coastal dune areas, and as a crop in monoculture on agricultural fields. In the Netherlands, T. coeruleus can be found both in the coastal dune areas and on agricultural fields. The interesting thing is that coastal dune populations of T. coeruleus are infected with parthenogenesis-inducing Wolbachia, while agricultural field populations are not infected with this bacterium. Therefore, we find asexual populations (only females) of T. coeruleus that reproduce through parthenogenesis in the Dutch dunes and sexual populations (males and females) of T. coeruleus on Dutch agricultural fields. Interestingly, all populations of T. coeruleus in Massachusetts (USA) and Southern France are infected with the same parthenogenesis-inducing Wolbachia. I am interested in the differences between these populations.
Asobara japonica (Hymenoptera) is a larval parasitoid of Drosophila flies and it occurs on many islands in Japan. As in T. coeruleus, some populations of A. japonica are infected with parthenogenesis-inducing Wolbachia, while other populations are not. While infected asexual populations are known from the two Japanese main islands, uninfected sexual populations are restricted to several small islands. The interesting thing about A. japonica is that asexual females sometimes produce a few males. We want to investigate why and how these males are produced. We are also interested in the effects of Wolbachia on these males.

Majeed Askari Seyhoei

cosupervised with Jacques van Alphen at Leiden University, The Netherlands

* Majeed defended his thesis on February 3rd, 2010*

In my PhD project, I studied the relationships between parasitoids, hosts and climate from an evolutionary point of view by using hymenopteran parasitoids as a model system. I used a comparative approach to study the variation in life-history traits of species and populations from different habitats. I showed that closely related species manipulate their host behaviour differently and allocate their essential resources to different life-history traits. Metabolic rate and energy reserves varied strongly among the species. Energy reserves were found to vary substantially between populations from different climate zones. A molecular study revealed genetic divergence between the populations. The pattern a divergence partially reflected variation in life-history among the populations. To conclude, I suggest that life-history traits of parasitoids are subject to natural selection pressures from both host and climate. Resource allocation and host manipulation in parasitoids is species specific and resource allocation is highly diverged among populations to fit habitat requirements.

Leptopilina clavipes

image Herman Berkhoudt

We sequenced the complete genomes of a sexual and an asexual lineage of this parasitoid wasp. The latter are asexual because they are infected by a parthenogenesis-inducing Wolbachia bacterium. This infection became established roughly 100,000 years ago. The comparison of the two genomes provides insight into the genomic consequences of asexual reproduction. In particular, we are interested in the accumulation of mutations and the associated decay of genes in asexuals.

Ongoing work includes:


  • Geuverink E, Kraaijeveld K, van Leussen M, Chena F, Pijpe J, Linskens MHK, Beukeboom LW, van de Zande L 2018 Evidence for involvement of a transformer paralog in sex determination of the wasp Leptopilina clavipes. Insect Molecular Biology 27: 78-795
  • Kraaijeveld K, Anvar Y, Frank J, Schmitz A, Bast J, Wilbrandt J, Petersen M, Ziesmann T, Niehuis O, de Knijff P, den Dunnen JT, Ellers J 2016 Decay of sexual trait genes in an asexual parasitoid wasp. Genome Biology and Evolution 8:3685-3995.
  • Kraaijeveld K, Zwanenburg B, Hubert B, Vieira C, de Pater S, van Alphen JJM, den Dunnen JT & de Knijff P 2012 Transposon proliferation in an asexual wasp. Molecular Ecology 21: 3898-3906.
  • Kraaijeveld K, Franco P, de Knijff P, Stouthamer R & van Alphen JJM 2011 Clonal genetic variation in a Wolbachia-infected asexual wasp: horizontal transmission or historical sex? Molecular Ecology 20: 3644-3652.
  • Kraaijeveld K., Franco P., Reumer B.M. & van Alphen J.J.M. 2009 Effects of parthenogenesis and geographic isolation on female sexual traits in a parasitoid wasp. Evolution 63: 3085-3096.
  • Reumer B., Kraaijeveld K. & van Alphen J.J.M. 2007 Selection in the absence of males does not affect male-female conflict in the parasitoid wasp Leptopilina clavipes (Hymenoptera: Figitidae). Journal of Insect Physiology 53: 994-999.