Jobs

    Four proposals for a PhD thesis

    1. Drivers of adaptation along an environmental gradient in the three-spined stickleback

    sticleback

    Vertebrate radiations go through a gradual process of differentiation along the axes of habitat, trophic morphology and communication, very often in that order. The three-spined stickleback has differentiated in the Lowlands along the habitat axis with anadromous populations inhabiting the coastal plain and freshwater populations inhabiting the rivers. It also has differentiated along the axis of trophic morphology with coastal populations having gill rakers adapted to small food particles and body armour defending against fish and bird predators. The axis of communication including feeding and nesting behavior and feromones has not been documented to date. You will characterise the phenotype of low and high growth response sticklebacks in the laboratory and identify through genomic profiling regions under selection pressure for behaviour. The research combines evolutionary, experimental and molecular biological approaches and has clear applications in aquaculture. The project is done in close collaboration with an expert in bioinformatics. Research funding is available through Excellence Financing by the KU Leuven.

    More information: Dr. Joost Raeymaekers (joost.raeymaekers@bio.kuleuven.be)
    Funding opportunities: FWO
    Relevant papers published by our team:

    1. Raeymaekers J.A.M., Wegner K.M., Huyse T., Volckaert F.A.M. (2011) Infection dynamics of the monogenean parasite Gyrodactylus gasterostei on sympatric and allopatric populations of the three-spined stickleback Gasterosteus aculeatus  Folia Parasitologica 58: 27-34
    2. Raeymaekers J.A.M., Raeymaekers D., Koizumi I., Geldof S., Volckaert F.A.M. (2009). Guidelines for restoring connectivity around water mills: a population genetic approach to the management of riverine fish. Journal of Applied Ecology 46: 562-571.
    3. Van Dongen S., Lens L., Pape E., Volckaert F.A.M., Raeymaekers J.A.M. (2009) Evolutionary history shapes the association between developmental instability and population-level genetic variation in three-spined sticklebacks. Journal of Evolutionary Biology 22: 1695-1707
    4. Raeymaekers J.A.M., Maes G.E., Geldof S., Hontis I., Nackaerts K., Volckaert F.A.M. (2008) Modelling genetic connectivity in sticklebacks as a guideline for river restoration. Evolutionary Applications 1: 475-488
    5. Raeymaekers J.A.M., Huyse T., Maelfait H., Hellemans B., Volckaert F.A.M. (2008) Community structure, population structure and topographical specialization of Gyrodactylus (Monogenea) ectoparasites living on sympatric stickleback species. Folia Parasitologica 55: 187-196
    6. Raeymaekers J.A.M., Van Houdt J.K.J., Larmuseau M.H.D., Geldof S., Volckaert F.A.M. (2007) Divergent selection as revealed by PST and QTL-based FST in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient. Molecular Ecology 16: 891-905.

    2. Biomarkers for enhanced, directed and sustainable selection of  European sea bass

    Seabass

    There is a great demand for sustainably bred fish with high food conversion ratios and feed with a low content in fish meal. Family selection of such fish is in progress, but it would be great if marker assisted selection could be implemented to shorten the selection time. This requires a good knowledge of the genome, and therefore the identification of regions under current selection and as target for enhanced selection. You will characterise the genomic characteristics of European sea bass undergoing selection regimes for growth, feed conversion and herbivory. The research combines evolutionary, molecular biological and bioinformatic approaches and has clear applications in aquaculture. Research funding is pending an EU grant application.

    More information: prof. Filip Volckaert (filip.volckaert@bio.kuleuven.be) and dr. Gregory Maes (Gregory.maes@bio.kuleuven.be)
    Funding opportunities: IWT
    Relevant papers published by our team:

    1. Souche E.L., Hellemans B., Van Houdt J.K.J., Volckaert F.A.M. (2012) Characterisation and validation of single-nucleotide polymorphism markers in expressed sequence tags of European sea bass. Molecular Ecology Resources
    2. Louro B.E., Passos A.,L., Souche E., Tsigenopoulos C., Beck A., Lagnel J., Bonhomme F., Cancela M.L., Cerda J., Clark M.S., Lubzens E., Magoulas A., Planas J., Volckaert F.A., Reinhardt R., Canario A. (2010) Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: characterization, tissue-specific expression and genetic markers. Marine Genomics 3: 179-191
    3. Guyon R., Senger F., Rakotomanga M., Sadequi N., Volckaert F.A.M., Hitte C. & Galibert F. (2010) A Radiation Hybrid map of the European sea bass (Dicentrarchus labrax) based on 1,581 gene markers: synteny analysis with model fish genomes. Genomics 96: 228-238
    4. Kuhl H., Beck A., Wozniak G., Canario A.V.M., Volckaert F.A.M., Reinhardt R. (2010) The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genetics 11 (68): 1-13
    5. Massault C., Hellemans B., Louro B., Batargias C., Van Houdt J., Canario A., Volckaert F.A.M.J., Bovenhuis H., Haley C., de Koning D.J. (2009) QTL for body weight, morphometric traits and stress response in European sea bass Dicentrarchus labrax. Animal Genetics 41: 337-345
    6. Chistiakov D.A., Tsigenopoulos C.S., Lagnel J., Yuanmei G., Hellemans B., Haley C.S., Volckaert F.A.M., Kotoulas G. (2008) A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L. Animal Genetics 39: 623-634
    7. Chistiakov D.A., Hellemans B., Volckaert F.A.M. (2006) Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture 255:1-29

    3. Vision-based life history decisions in a marine goby

    Sandgoby

    Survival in nature depends on the possibility to adapt to environmental conditions, or to move to better places. Observing how marine organisms do so is particularly difficult. However, the study of their molecules can learn a lot about how they are adapted to a certain environment, and which movements they make through their lifetime. In fishes, otolith microchemistry can tell where an individual fish was born and how it migrated. In addition, genomic techniques enable to investigate its vision genes such as rhodopsine, and whether it is adapted to see well in clear waters, turbid waters, or both. Together, otolith microchemistry and rhodopsine variation might reveal whether or not individuals take vision-based life history decisions: do they move to clear waters when their vision is not well adapted to turbidity, and do they move to more turbid waters to feel more safe when their vision allows to find food there? We investigate these decisions in marine gobies migrating back and forth the North Sea and the Scheldt estuary. You will characterize the population dynamics and genomic profile of local populations of the sand goby and implement expression profiling in common garden experiments. Selective breeding of key populations might be used to identify the genes and gene regions under selection. The research combines field sampling, evolutionary and molecular biological approaches, and has implications for conservation biology and coastal zone management. Research funding is pending a BELSPO grant application.
    More information: Dr. Joost Raeymaekers (joost.raeymaekers@bio.kuleuven.be); Dr. Maarten Larmuseau (maarten.larmuseau@bio.kuleuven.be); prof. Filip Volckaert (filip.volckaert@bio.kuleuven.be)
    Funding opportunities: FWO
    Relevant papers published by our team:

    1. Larmuseau M., Raeymaekers J.A.M., Hellemans B., Van Houdt J.K.J., Volckaert F.A.M. (2010) Mito-nuclear discordance in the degree of population differentiation in a marine goby. Heredity 105: 532-542
    2. Larmuseau M.H.D., Huyse T., Vancampenhout, K., Van Houdt, J.K.J., Volckaert F.A.M. (2010) High molecular diversity in the rhodopsin gene in closely related goby fishes: A role for visual pigments in adaptive speciation? Molecular Phylogenetics and Evolution 55: 689-698
    3. Larmuseau M.H.D., Vancampenhout, K., Raeymaekers J.A.M., Van Houdt, J.K.J., Volckaert F.A.M. (2010) Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby, Pomatoschistus minutus. Molecular Ecology 19: 2256-2268
    4. Larmuseau M.H.D., Van Houdt J.K.J., Guelinckx J., Bart Hellemans B., Volckaert F.A.M. (2009) Distributional and demographic consequences of Pleistocene climate fluctuations for a marine demersal fish in the north-east Atlantic. Journal of Biogeography 36: 1138-1151
    5. Guelinckx J., Maes J., Geysen B., Ollevier F. (2008) Estuarine recruitment of a marine goby reconstructed with an isotopic clock. Oecologia 157: 41-52.
    6. Maes J., Stevens M. Ollevier F. (2005) The composition and community structure of the ichthyofauna of the upper Scheldt estuary: synthesis of a 10-year data collection (1991-2001). Journal of Applied Ichthyology 21: 86-93

    4. Parasite-driven evolution in Lake Tanganyika cichlids

    Tropheus morii

    Cichlid fish of the East-African Great Lakes are the most diverse species assemblage of vertebrates on our planet. Even though they have become a model for speciation research, how and why they reached this enormous diversity remains difficult to explain based on current insights. One theory is that cichlids evolved through habitat diversification (e.g. adaptation to a substrate type), trophic diversification (evolution of different feeding strategies and adaptation to a specific diet) and communication diversification (e.g. evolution of different social interactions including colour- and odour-based mate recognition). However, different habitats, diets and social interactions might also lead to exposure to different parasite communities. Parasites challenge their host’s immune system, and represent strong agents of natural selection. Moreover, parasites might also contribute to sexual selection through immunity-based mate choice (which in cichlids is reflected in brightness and coloration). The combined effect of natural and sexual selection on a trait (in this case the immune system) has the potential to accelerate speciation. Therefore cichlid diversification might essentially be parasite-driven, but this hypothesis has received little attention. Using a combination of genomics and field-based studies, we investigate the contribution  of parasites to the diversification of Lake Tanganyika cichlids.

    More information: Dr. Joost Raeymaekers (joost.raeymaekers@bio.kuleuven.be)
    Funding opportunities: FWO; one year of funding is available
    Relevant papers published by our team:

    1. Gillardin C, Vanhove M.P.M., Pariselle A., Huyse T., Volckaert F.A.M. (2012) Ancyrocephalidae (Monogenea) of Lake Tanganyika: II: description of the first Cichlidogyrus spp. Parasites from Tropheini fish hosts (Teleostei, Cichlidae). Parasitological Research 110: 305-313.
    2. Van Steenberge M., Vanhove M.P.M., Muzumani Risasi D., Mulimbwa N’Sibula T., Muterezi Bukinga F., Pariselle A., Gillardin C., Vreven E., Raeymaekers J., Huyse T., Volckaert F.A.M., Nshombo Muderhwa V., Snoeks J.  (2012) A recent inventory of the fishes of the north-western and central western coast of Lake Tanganyika (Democratic Republic of Congo). Acta Ichthyological et Piscatoria 41: 201-214.

  • Excellent graduate students may apply for FWO-Vlaanderen or IWT grants
  • Excellent postdocs may always apply for FWO-Vlaanderen or KULeuven grants. EU Marie Curie and other international grant applications are welcome.