Karine Van Doninck Lab
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Laboratory of Evolutionary Genetics and Ecology (LEGE)


Pr. Karine Van Doninck - Download the CV
Contacts: karine.vandoninck@unamur.be; Tel. +32 81/72 44 07; Fax. +32 81/72 43 62

PhD (in 2003) jointly from the laboratory of Cellular Genetics at the Free University of Brussels (VUB) with Prof. Micheline Kirsch-Volders and the laboratory of Freshwater Biology at the Royal Belgian Institute of Natural Sciences (RBINSc) with Dr. Koen Martens and Dr. Isa Schön. Post-Doctoral researcher (2003-2006) in the laboratory of Prof. Matthew Meselson in the Molecular and Cellular Department (MCB) at Harvard University, USA. A second postdoc (2006-2007) on a Marie-Curie (IEF) grant in the laboratory of Dr. Yannis Michalakis at GEMI-IRD (France). Since September 2007 I am an Associate Professor at the University of Namur and founded the Laboratory of Evolutionary Genetics and Ecology (LEGE). My research interests integrate molecular genetics, organism evolution, evolution of reproductive modes, comparative genomics and invasive species (see research). Since September 2009 I received the grade of Full Professor at UNamur.

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POST-DOC

Jonathan Marescaux / Contacts: jonathan.marescaux@unamur.be; Tel. +32 81/72 43 92

Jonathan Marescaux is a molecular ecologist specialized in biological conservation. He conducted his PhD under Karine Van Doninck supervision in the LEGE laboratory (UNamur) on the invasion of Western European freshwater systems by the quagga mussel (Dreissena rostriformis). More specifically, this study investigated the distribution of quagga mussels in Belgium, resolved the invasion pathways of this species in Western Europe and assessed the impact of Dreissena on the ecosystem. Thanks to expertise, Jonathan was also involved in several research projects studying (i) the main causes of fish stock decline in Meuse River; (ii) the invasion of quagga mussels in the United Kingdom; and (iii) the genetic structure of the African buffalo. After his PhD he was during 8 months an external consultant on a project funded by the Firestone Building Products Company to describe aquatic ecosystems in Belgium and New Zealand. In November 2015, Jonathan Marescaux obtained a First Spin-Off financial support from the Walloon Region to create an engineering and consultancy enterprise.

>> Selected recent publications:

Marescaux J., Latli A., Lorquet J., Virgo J., Van Doninck K. and Beisel J.-N. (2016) Benthic macro-invertebrate fauna associated with Dreissena mussels in the Meuse River: from incapacitating relationships to facilitation. Aquatic Ecology, doi:10.1007/s10452-015-9540-5
Marescaux J., von Oheimb K.C.M., Etoundi E., von Oheimb P.V., Albrecht C., Wilke T and Van Doninck K (2016) Unraveling the invasion pathways of the quagga mussel (Dreissena rostriformis) into Western Europe. Biological Invasions, doi:10.1007/s10530-015-1005-1
Marescaux J., Falisse E., Lorquet J., Van Doninck K., Beisel J.-N. and Descy J.-P. (2016) Assessing filtration rates of invasive filter-feeder bivalves: dependence on algae concentration and seasonal factors. Hydrobiologia, doi:10.1007/s10750-016-2764-0

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Jitendra Narayan / Contacts: jitendra.narayan@unamur.be Tel. +32 81/72 43 59

I completed my PhD work at the Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Wales, UK, under the supervision of Dr Denis Larkin and Dr Neil McEwan. My PhD research work centered around the chromosomal breakpoint identification in amniote genomes, and in particular connecting Evolutionary Breakpoint Regions (EBRs) to the changes gained by each species during the course of evolution.
I joined Karine Van Doninck laboratory in 2016 as a bio-informatician pursuing comparative genomic studies in order study the genome dynamics of the bdelloid rotifer lineages sequenced after cycles of desiccation/rehydration. We also assemble new bdelloid genomes. I will also develop computational pipelines to follow the dynamics of chromosomal rearrangements. You can find more at my website http://bioinformaticsonline.com/profile/admin

>> Selected recent publications:

Zhang, G., et al. (2014) Comparative genomics reveals insights into avian genome evolution and adaptation, Science, 346 (6215), 1311-1320. Narayan J. is co-author on this publication
Groenen, M.A. et al. (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393-398. Narayan J. is co-author on this publication

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Matthieu Terwagne / Contacts: matthieu.terwagne@unamur.be Tel. +32 81/72 43 59

I graduated as a molecular and cellular biologist (2006) and received my PhD (2011) as a FNRS Research Fellow from the University of Namur for work done under the supervision of Prof Jean-Jacques Letesson on host and pathogen adaptations during infection.

I joined the LEGE in October 2014 as a FNRS Postdoctoral Researcher and I am currently using genetic and genomic approaches to decipher the mechanisms of horizontal gene transfer in Bdelloid rotifers to try to make sense of the confusing problem of their asexual evolution.

>> Selected recent publications:

Terwagne M., Ferooz J., Rolan H.G., Sun Y.H., Atluri V., Xavier M.N., Franchi L., Núñez G., Legrand T., Flavell R., De Bolle, X., Letesson JJ. and Tsolis R. (2013) Innate immune recognition of flagellin limits systemic persistence of Brucella. Cell Microbiol. 15(6):942-60.
Terwagne M., Mirabella A., Lemaire J., Deschamps C., De Bolle X. and Letesson J-J. (2013) Quorum Sensing and Self-Quorum Quenching in the Intracellular Pathogen Brucella melitensis. PLoS ONE 8, p. e82514.
Mirabella A., Terwagne M., Zygmunt M.S., Cloeckaert A., De Bolle X., Letesson JJ. (2013) Brucella melitensis MucR, an orthologue of Sinorhizobium meliloti MucR, is involved in resistance to oxidative, detergent and saline stresses and cell envelope modifications. J Bacteriol. 195(3):453-65.

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Marc Lliros / Contacts: marc.llirosdupre@uclouvain.be Tel. +32 81/72 43 59

Marc Llirós is microbial ecologist that is now engaged to tackle with the molecular mechanisms behind the genomic rearrangements in the ameiotic bdelloid rotifer Adineta vaga.
However, he has been involved in several research projects in order to analyse the microbial diversity (both bacteria and archaea) in a wide range of environments covering from microbial mats and coastal wetlands to stratified freshwater lakes and crude oil fields by using classical and molecular tools trying to decipher the role of microbes in global biogeochemical cycles.

>> Selected recent publications:

Llirós M, Inceoğlu Ö, García-Armisen T, Anzil A, Leporcq B, Pigneur LM, Viroux L, Darchambeau F, Descy JP and Servais P. (2014) Bacterial community composition in three freshwater reservoirs of different alkalinity and trophic status. PLoS ONE 9(12) e116145.
Llirós M, Trias R, Borrego C & Bañeras L (2013) Specific Archaeal communities are selected on the root surfaces of Ruppia spp. and Phragmites australis. Wetlands 34, 403 – 411.
Lenchi N, Inceoğlu Ö, Kebbouche-Gana S, Gana ML, Llirós M, Servais P & García-Armisen T. (2013). Diversity of microbial communities in production and injection waters of Algerian Oilfields revealed by 16S rRNA gene amplicon 454 pyrosequencing. PLoS ONE, 8(6), e66588.

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Marie Cariou / Contacts: marie.cariou@unamur.be Tel. +32 81/72 43 59

During my PhD at the Laboratory of Biometry and Evolutionary Biology at the University of Lyon, under the supervision of Sylvain Charlat and Laurent Duret (2011-2015), I studied the impact of an endocellular bacteria, Wolbachia, on the evolution of its Arthropod hosts. More specifically, I looked for effects of these maternally transmitted symbionts on host mitochondrial genomes, to which they are linked within the cytoplasm, at a global scale, among hundreds of species from French Polynesia. Since september 2015, I work as a Post-doctoral researcher at the University of Namur, with Pr. Karine van Doninck, on the evolution of Bdelloid rotifers genomes and of their genomic peculiarities. I am generally interested in studying the evolution of genomes and on processes that shape this evolution at different scales. Notably, I worked on the developpement and analysis of RADseq markers, a technic which uses high throughput sequencing for reduced representation genomics and obtention of population genomics markers.

>> Selected recent publications:

Henri H, Cariou M, Terraz G, Martinez S, El Filali A, Veyssiere M, Duret L, Charlat S (2015) Optimization of multiplexed RADseq libraries using low-cost adaptors, Genetica, vol. 143 pp.139-43, DOI
Cariou M, Duret L, Charlat S (2013) Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization, Ecology and Evolution, vol. 3 pp.846-852, DOI

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Boris Hespeels / Contacts: boris.hespeels@unamur.be; Tel. +32 81/72 42 86

In 2009, I started my PhD under supervision of Pr K. Van Doninck. With a Molecular and Cellular biology background, my PhD project focused on following points: How desiccation is affecting genomic integrity of bdelloid rotifers Adineta vaga ? How horizontal gene transfers contribute to bdelloids biology? How to resist against desiccation and radiations? How to promote bdelloid rotifers as model organism for stress resistance studies? As a teaching assistant of Pr K. Van Doninck, I give the following practical works at the University of Namur: zoology, bioinformatics in genomics, physiology and marine biology.

>> Selected recent publications:

Hespeels, B., Li, X., Flot, J-F., Pigneur, L-M., Malaisse, J., Da Silva, C. & Van Doninck, K. Against all odds: trehalose-6-phosphate synthase and trehalase genes in the bdelloid rotifer Adineta vaga were acquired by horizontal gene transfer and are upregulated during desiccation. PLoS ONE. 10, 7, e0131313. 2015. (I.F.: 3,53)
Hespeels, B, Flot, J-F, Derzelle, A & Van Doninck, K. Evidence for Ancient Horizontal Gene Acquisitions in Bdelloid Rotifers of the Genus Adineta. Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life. P. Pontarotti (ed.) Ed. Springer International Publishing Switzerland, 2014.
Hespeels B, Knapen M, Hanot-Mambres D, Heuskin AC, Pineux F, Lucas S, Koszul R, Van Doninck K. Gateway to genetic exchange? DNA double-strand breaks in the bdelloid rotifer Adineta vaga submitted to desiccation. Journal of Evolutionary Biology, 2014 (I.F.: 3.479)
Flot, J-F; Hespeels, B; Li, X; Noel, B; Arkhipova, I; Danchin, E; Hejnol, A; Henrissat, B; Koszul, R; Aury, J-M; Barbe, V; Barthélémy, R-M; Bast, J; Bazykin, G A.; Chabrol, O; Couloux, A; Da Rocha, M; Da Silva, C; Gladyshev, E; Gouret, P; Hallatschek, O; Hecox-Lea, B; Labadie, K; Lejeune, B; Piskurek, O; Poulain, J; Rodriguez, F; Ryan, J F.; Vakhrusheva, O A.; Wajnberg, E; Wirth, B; Yushenova, I; Kellis, M; Kondrashov, A S.; Mark Welch, D.; Pontarotti, P; Weissenbach, J; Wincker, P; Jaillon, O; Van Doninck, K. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature, 2013. (I.F.: 38,2): doi:10.1038/nature12326

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PhD Students


Nicolas Debortoli, FRIA PhD student / Contacts: nicolas.debortoli@unamur.be Tel. +32 81/72 43 92

I have always been interested in organisms that have chosen alternative strategies to survive and diversify. I have therefore studied biology at the University of Namur (Belgium) and I specialized in molecular ecology and evolution during my master degree. I wrote a master thesis in the Laboratory of Evolutionary Genetics and Ecology (LEGE) about the genetic diversity of the asexual bdelloid rotifers at the local scale. Then, I went to Stanford University for a 5 months internship on dependent-lineage harvester ant populations. Asexuality and eusociality are questions that remain misunderstood in evolution and are thus of most interest for me.
My PhD thesis aims at understanding how degenerate tetraploidy and desiccation enable bdelloid rotifers to survive, disperse and diversify in the absence of sexual reproduction. The main chapters of the thesis will be (1) to develop new tools to study the genetic diversity, genome dynamics and distribution of bdelloid rotifers at the local scale and (2) the bdelloid communities spatio-temporal dynamics ; (3) understand the mechanisms underlying molecular adaptation and survival of bdelloid rotifers through comparative genomics approach. Different tools from molecular biology to bioinformatics and ecology are used.

>> Selected recent publications:

Debortoli, N., Li, X., Eyres, I., Fontaneto, D., Hespeels, B., Tang, C. Q., Flot, J.-F., & Van Doninck, K. (2016). Genetic exchange among bdelloid rotifers is more likely due to horizontal gene transfer than to meiotic sex. Current Biology, 26(6), 723-732.
Gordon DM, Pilko A, Debortoli N and Ingram K, 2013. Does an ecological advantage produce the asymmetric lineage ratio in a harvester ant population? Oecologia, Volume 173, Issue 3, pp 849-857. DOI 10.1007/s00442-013-2690-z.

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Alessandro Derzelle, FNRS PhD student / Contacts: alessandro.derzelle@unamur.be Tel. +32 81/72 43 92

With a master degree in ecology and biodiversity, I am currently writing a PhD thesis (FNRS grant, 2014) on gene copy number variation in the bdelloid rotifer model Adineta vaga. My work aims at understanding the rate of gene duplication in an ancient asexual model and the copy number variation rate following desiccation cycles.
These rates will be evaluated through experimental evolution studies. A particularly interesting aspect of my research is the link between gene copy number variation and the ability of A. vaga to survive desiccation and repair the hundreds of DNA double-strand breaks induced.

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FORMER RESEARCHERS

Jean-François Flot / Contact: jean-francois.flot@ds.mpg.de

PhD (in 2007) from the Muséum national d’Histoire naturelle in Paris on the molecular systematics of scleractinian corals (PhD advisor Prof. Simon Tillier). First postdoc (2008-2010) with Prof. Sharmishtha Dattagupta at the Courant Research Centre “Geobiology” (University of Göttingen, Germany) investigating the taxonomy and symbioses of cave-dwelling ampipods. Second postdoc (2010-2013) jointly at the University of Namur with Prof. Karine van Doninck and at Genoscope (Evry, France) assembling and analyzing the genome of the bdelloid rotifer Adineta vaga. Current post-doc with Dr. Oskar Hallatschek on biological physics and evolutionary dynamics at the University of Göttingen (Germany).
Author of the online programs Champuru (http://www.mnhn.fr/jfflot/champuru/) and SeqPHASE (http://www.mnhn.fr/jfflot/seqphase/).
Research interests: phylogenetics, genome evolution, bioinformatics, species delimitation, coral reefs, subterranean environments

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Xiang Li / Contact: xiang.dolphin@gmail.com

PhD FRIA student (2007-2008) at the Unit of Evolutionary Genetics (UEG) at the Free University of Brussels (ULB) with Prof. Michel C. Milinkovitch on the population genetics of marine mammals. PhD FRIA student (2008-present) in the laboratory of Prof. Karine Van Doninck at the University of Namur (UNamur) on the population genetics and comparative genomics of bdelloid rotifers.

Research interests: population genetics, molecular evolution, ancient asexuality of bdelloid
rotifers, conservation, comparative anatomy and ecology of marine mammals

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Lise-Marie Pigneur / Contact: lise-marie.pigneur@unamur.be

I am passionately fond of animals and plants since my childhood. I therefore studied biology at the University of Namur (Belgium) and specialized in freshwater ecology. For my master thesis I spent 4 months along Congo river and studied taxonomy and biology of African elephantfish (Mormyridae). There I have been puzzled by the complexity of defining a species. I graduated in 2005 and started working as a teaching assistant at the University of Namur, combining teaching activities and PhD research. For my PhD thesis, I decided to work on invasive organisms: the basket clams of the genus Corbicula spp. Interestingly, these odd creatures reproduce through androgenesis: during fertilization, the maternal chromosomes are extruded from the oocyte and the unreduced sperm provides the complete nuclear genome to the offspring! I am studying phylogeny and phylogeography of these clams and the role of androgenesis in their invasiveness. I am also interested in assessing the impact of Corbicula clams on aquatic ecosystems, here the Meuse river. I am particularly interested in biodiversity, taxonomy, phylogeny, phylogeography and evolution.

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Emilie Etoundi / Contact: emilie.etoundi@unamur.be

Master (2011) in Biochemistry, Cell and molecular biology at the University of Namur. PhD student at the University of Namur in LEGE lab with Pr. Karine Van Doninck. PhD thesis about androgenesis in the bivalve genus Corbicula.

Research interests: Evolutionary biology, evolution of reproduction modes, parasitism evolution, cytology, molecular ecology

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MASTER STUDENTS

2016
Brieuc Delcommenne, Master BBMC UNamur
Claire Stulemeijer, UCL-UNamur

2015
Maud Radelet, Master BBMC UNamur
Christophe Vanhaver, Master BBMC UCL

2014
Benjamin Dujardin, Master BOE UNamur

2012
Benjamin Lejeune, Master BOE UNamur
Caroline Laurent, Master BOE UNamur
Audrey Vokaer, Master BOE UNamur

2011
Nicolas Debortoli, Master BOE UNamur
Manon Knapen, Master BOE UNamur
Alessandro Derzelle, Master BOE UNamur

2010
Emilie Etoundi, Master BBMC UNamur
Elodie Falisse, Master BOE UNamur
 
2009
Delphine Hanot-Mambres, Master BBMC
Jonathan Marescaux, Master BOE

2008
François Renoz, Master BOE

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TECHNICAL & ADMINISTRATIVE STAFF

Yves Mine - Computer support
Contacts : yves.mine@unamur.be Tel. +32 81/72 43 62

Julie Virgo - Laboratory technician
Contacts : julie.virgo@unamur.be Tel +32 81/72 43 92

Catherine Demazy - Laboratory technician
Contacts : catherine.demazy@unamur.be Tel +32 81/72 43 59

UNamur • University of Namur
Postal address : rue de Bruxelles 61, B-5000 Namur, Belgium