Theoretical population genetics for current biological systems

Solenn Stoeckel, INRA researcher in theoretical and applied population genetics.

  Contact:

       INRA/AgroCampus Rennes/Université Rennes1
       Institute for Genetics, Environment and Plant Protection, UMR 1349
       Team Demecology: Dynamics, Evolution, Modelisation, Ecology

  Domaine de la Motte, BP 35327, 35653 Le Rheu cedex, France
  +33 (0)2 23 48 70 83
  solenn.stoeckel#at#inra.fr

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       Publications

       Software and libraries

       ORCID Researcher ID

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Ant Aphid ladybug


Cherry trees


Research Interests

I'm interested in understanding the current intrinsic (biological traits) and extrinsic (environmental) factors that determine the ability of populations to evolve before our eyes.

To achieve these goals, I develop algorithmic and mathematical predictive models in population genetics, develop methods and analytical tools, propose efficient methodologies and frameworks, acquire and analyse field populations using current genomic advances for genotyping individuals to exploit hereditary (genetic footprints and phenotypes) information to answer fondamental and applied (eg conservation, management) questions in Ecology and Evolution.  

Main paradigm
     -
Theoretical and applied Population Genetics
Scientific interests
     - Effects of reproductive modes (specially partial clonality) on the dynamics of genetic diversity.
     - Genetic and phenotypic divergences in peri- and para-patric conditions
     - Quantitative inference of evolutionary forces acting on contemporary populations

Implemented tools:
     - Mathematics of stochastic processes (Markov chain, SDE, diffusion limits)
     - Numerical intensive calculations (parallelization, GPGPU)
     - Advanced statistics (Bayesian, machine learning)
     - Genotyping and automated sequencing of experimental and field populations





Current Projects and collaborations

In review:
    • ANR Clonix2D (resp. S.Stoeckel),The genetic consequences of partial clonality in populations colonizing new areas.
    • Russian Science Foundation ACTINIA (resp. E.Bocharova, VNIRO): inferring the rates of clonality and evolutionary histories of russian arctic anemone populations.

  • INVAMAT (INRA-SPE, 2018-2020): Evolvability of invasive species: Modelling the demogenetics of invasive populations in spatially-explicit contexts. Resp. ME Orive (University of Kansas) & S.Stoeckel (INRA Rennes).
  • GRACILARIA (FONDECYT-CONOCYT 2018-2021): Deciphering the complex evolutionary history of a domesticated red alga in Pacific ocean using population genomics. Resp. ML Guillemin (Universidad Austral de Chile).
  • STARTAUP (Ecophyto II, 2017-2020): understanding the current evolutionary trajectories of wireworms to propose alternative control strategies and limit damage on crops. Resp. R.LeCointe (INRA Rennes)
  • CLONIX (ANR, 2012-2016): An in-depth review of the Genetics of Populations and the Genomics of Clonal Organisms. Resp. S Arnaud-Haond (Ifremer Sète).
  • DevMAP (INRA, 2015-2016): Develop Automated Morphometry to help measure the impact of anthropogenic landscapes on the life traits of invasive species and crop auxiliaries. Resp N.Parisey (INRA Rennes)
  • DIVAPHID (FRB, 2010). Genetic architecture underpinning ecological specialization and reproductive isolation. Resp. S.Stoeckel (INRA Rennes).
  • AphidSEX (INRA-SPE, 2010-2012). Comparative evolution of genomic regions under divergent selection between sexed and asexual aphid lines. Resp. C.Rispe & S.Stoeckel (INRA Rennes).
  • SESAME (INRA-SMaCH, 2013-2015): Landscape dynamics and pest management. Resp N.Parisey (INRA Rennes).
  • PEERLESS (ANR, 2012-2016): Predictive Ecological Engineering for Landscape Ecosystem Services and Sustainability. Resp. for DEMECOLOGY N.Parisey
  • FORgwas (INRA-Agreenium-Uppsala Universitet, 2012): developing a new method to search for signs of selection in complete genome data. Resp M.Jakobsson (Uppsala Universitet) & S.Stoeckel (INRA Rennes)
  • GW-Aphid (ANR Genomics and Plant Biotechnology, 2010-2012): Association of Genome Scan, QTL and transcriptomic methods to identify genes involved in the biological variability of reproduction patterns in aphids. Resp D.Tagu (INRA Rennes).
  • Host-GWAS (INRA-SPE, 2007-2009): Scanning pea aphid genomes for loci involved in host-plant preferences. Resp JC Simon (INRA Rennes)
  • GeneticDiversity (BRG, 2005-2006): Reasoned sampling strategies to capture genetic diversity and its structuring in natural populations. Resp S. Brachet (ENGREF) & S.Mariette (IRSTEA Orleans)
  • Vilmorin seed project (2005): Evaluation of the genetic diversity of a cherry seed orchard, recommendations for obtaining a quality label. Resp INRA & IRSTEA Orleans.
  • MACULINEA (Natura 2000, 2000): National plan of action for the maintenance of Maculinea. Resp Regional natural park of Brenne & University of Tours.

maculineagentianemyrmica
 

strain desease

Alumni

Post-docs: Dr Ronan Becheler (2015-2016, Roscoff & Universidad Austral de Chile), Dr Romuald Rouger (2014-2016), Dr Diane Bailleul (2015, Ifremer Sete), Dr Julie Jaquiéry-Evanno (2014).

PhD students: Luis Portillo (2017-, UMR ESE Rennes), Dr Pierre Nouhaud (2011-2014), Dr Katja Reichel (2012-2015)

DESU (1 year of training researches before a PhD): Clément Goubert (2011-2012), Mélodie Kunegel-Lion (2013-2014)

Master students: Valentin Bahier, Clément Barthélémy, , Nina Bernard, Chloé Larose, Cédric Midoux, Pierre Nouhaud, Barbarra Porro.



Teaching

  • Co-leader with G.Evanno of the Population Genetics and Genomics Course (Master2 MODE and EFCE, U.Rennes1)
  • Teacher of the Stochastic Models and Mathematics for Evolution Course (Master2 MODE, U.Rennes1)
  • Teacher Theoretical and Applied Scientific Method and Critical thinking Course (U.Rennes1, General public lecture)
  • Teacher Evolution of reproductive modes (Master2 EFCE, U.Rennes1, AgrocampusOuest)
  • Leader Population genetics for professional and scientific use (INRA Formation)
  • Leader Python for scientific calculations and analyses, discovery and advanced sessions (INRA Formation)
  • Teacher Why reproduce and die? An evolutionary view of death? (General public lecture)
  • Teacher Why Evolutionary theory hurts societies but open vast areas for human progress? (General public lecture)
  • Animator Experiencing Evolution with your hands! Beans versus Kids. (General public lecture)
critical mind

forest path


Positions and Education

  • Since 2017, Researcher in the Demecology Team (INRA Rennes).
  • Since 2012, Researcher in the Ecology and Genetics of Insects group (INRA Rennes). 
  • 2012, 6-months visiting Mattias Jakobsson Lab (Evolutionary Biology Centre, Uppsala Universitet).
  • Since 2007, young researcher at Bio3P (INRA Rennes).
  • 2006-2007, temporary lecturer at UPMC (Paris 6 University).
  • 2002-2006, ENGREF (AgroParisTech) PhD at Ecology, Systematics and Evolution (University Paris XI), grant Cemagref/Region Centre. S.Mariette and N.Frascaria (Supervisors).
  • 2000-2002, Master Ecology and Evolution at Insect Biology Research Institute (University of Tours).
    • Reproductive modes of Cardiocondyla elegans
    • Landscape and behavioural ecology of Maculinea alcon
    • Modeling the dynamics of rabies epidemics in an metapopulation of foxes

Publications

  1. Becheler R, Masson JP, Arnaud-Haond S, Halkett F, Mariette S, Guillemin ML, Valéro M, Destombe C, Stoeckel S (2017). ClonEstiMate, an accurate Bayesian method to estimate the rates of clonality using using time populations genotyping. Molecular Ecology Resources, 17, e251–e267.
  2. Montecinos AE, Guillemin M-L, Couceiro L, Peters AF, Stoeckel S & Valero M (2017). Hybridization between two cryptic filamentous brown seaweeds along the shore: analysing pre- and postzygotic barriers in populations of individuals with varying ploidy levels. Molecular Ecology, 26, 3497–3512.
  3. Rouger R, Reichel K, Malrieu F, Masson J-P, Stoeckel S (2016). Effects of complex life cycles on genetic diversity: cyclical parthenogenesis. Heredity, 117 (5), 336-347.
  4. Reichel K, Masson J-P, Malrieu F, Arnaud-Haond S, Stoeckel S (2016). Rare sex or out of reach equilibrium? The dynamics of FIS in partially clonal organisms. BMC Genetics 17, 1-16.
  5. Bailleul D, Stoeckel S, Arnaud-Haond S (2016). RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R. Methods in Ecology and Evolution, 7, 966–970.
  6. Reichel K, Bahier V, Midoux C, Parisey N, Masson JP, Stoeckel S (2015). Interpretation and approximation tools for big, dense Markov chain transition matrices in population genetics. Algorithms for Molecular Biology 10, 1-14.
  7. Gilabert A, Dedryver CA, Stoeckel S, Plantegenest M, Simon JC (2015). Longitudinal clines in the frequency distribution of'super-clones' in an aphid crop pest. Bulletin of Entomological Research 105 (6), 694-703.
  8. Jaquiery Evanno J, Stoeckel S, Larose C, Nouhaud P, Rispe C, Mieuzet L, Bonhomme J, Mahéo F, Legeai F, Gauthier JP, Prunier-Leterme N, Tagu D, Simon JC (2014). Genetic control of contagious asexuality in the pea aphid. Plos Genetics, 10 (12), e1004838
  9. Stoeckel S, Masson J-P (2014). The exact distributions of FIS under partial asexuality in small finite populations with mutation. PloS One 9 (1), e85228
  10. Lander TA, Klein EK, Stoeckel S, Mariette S, Musch B, Oddou-Muratorio S (2013). Interpreting realized pollen flow in terms of pollinator travel paths and land-use resistance in heterogeneous landscapes. Landscape Ecology, 28 (9), 1769-1783.
  11. Jaquiéry Evanno J, Rispe C, Roze D, Legeai F, Le Trionnaire G, Stoeckel S, Mieuzet L, Da Silva C, Poulain J, Prunier Leterme N, Segurens B, Tagu D, Simon J-C (2013). Masculinization of the X chromosome in the pea aphid. Plos Genetics, 9 (8).
  12. Dussert Y, Remigereau M -S, Fontaine MC, Snirc A, Lakis G, Stoeckel S, Langin T, Sarr A, Robert T (2013). Polymorphism pattern at a miniature inverted-repeat transposable element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet. Molecular Ecology, 22 (2), 327 - 340.
  13. Jaquiéry Evanno J, Stoeckel S, Rispe C, Mieuzet L, Legeai F, Simon J-C (2012). Accelerated evolution of sex chromosomes in aphids, an X0 System. Molecular Biology and Evolution, 29 (2), 837 - 847.
  14. Stoeckel S, Klein EK, Oddou-Muratorio S, Musch B, Mariette S (2012). Microevolution of S-allele frequencies in wild cherry populations: respective impacts of negative frequency dependent selection and genetic drift. Evolution 66 (2), 486-504.
  15. Jaquiéry J, Stoeckel S (co-premier auteur), Nouhaud P, Mieuzet L, Mahéo F, Legeai F, Bernard N, Bonvoisin A, Vitalis R, Simon J-C (2012). Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex. Molecular Ecology, 21 (21), 5251-64.
  16. Simon JC, Stoeckel S, Tagu D (2010). Evolutionary and functional insights into reproductive strategies of aphids. Comptes Rendus Biologies. volume 333, issue 6-7, pages 488-496.
  17. Villate L, Esmenjaud D, Van Helden M, Stoeckel S, Plantard O (2010). Genetic signature of amphimixis allows for the detection and fine scale localization of sexual reproduction events in a mainly parthenogenetic nematode. Molecular Ecology, volume 19, issue 5, pages 856-873.
  18. Navascués M, Stoeckel S, Mariette S. (2010). Genetic diversity and fitness in small populations of partially asexual, self-incompatible plants. Heredity, volume 104, issue: 5, pages: 482-492.
  19. Gilabert A, Simon J-C, Mieuzet L, Halkett F, Stoeckel S, Plantegenest M, Dedryver CA. 2009. Climate and agricultural context shape reproductive mode variation in an aphid crop pest. Molecular Ecology, volume 18, pages 3050-3061.
  20. Stoeckel S, Castric V, Mariette S, Vekemans X (2008). Unequal allelic frequencies at the self-incompatibility locus within local populations of Prunus avium L.: an effect of population structure? Journal of Evolutionary Biology, Volume 21, Issue 3, Pages 889-899.
  21. Peccoud J, Figueroa C, Silva A, Ramirez C, Mieuzet L, Bonhomme J, Stoeckel S, Plantegenest M, Simon JC (2008). Host range expansion of an introduced insect pest through multiple colonisations of specialized clones. Molecular Ecology, volume 17, issue 21, pages: 4608-4618.
  22. Mariette S, Balsemin E, Stoeckel S, Tavaud M, Le Bouler H, Santi F, Verger M (2007). Parental participation in progeny and effective population sizes in experimental seed orchards of an insect-pollinated tree species, the wild cherry Prunus avium L. (Batsch). Annals of Forest Science, volume 64, pages 533-539.
  23. Stoeckel S, Mariette S, Grange J, Bilger I, Frascaria-Lacoste N (2006). Heterozygote excess in a self-incompatible and partially clonal forest tree species —Prunus avium L. Molecular Ecology, volume 15, pages 2109-2118.
  24. Brachet S, Bastien C, Bilger I, Buret C, Dufour J, Grange J, Guérin V, Jorge V, Leguerroué B, Lesage-Descauses MC, Leveque L, Mardare I, Mariette S, Musch B, Sanchez L, Stoeckel S, Villar M, Santi F (2006) Stratégies raisonnées d’échantillonnage pour capturer la diversité génétique et sa structuration dans les populations naturelles – Application aux mesures de gestion conservatoire. Les Actes du BRG, volume 6, p. 211-230. (alphabetic order out of first author)
  25. Mercier J-L, Jérôme C, Darrouzet E, Stoeckel S (2002) Rôle des mâles dans la reproduction chez Cardiocondyla elegans (Formicidae:myrmicinae). Actes Coll. Insectes Sociaux, 5, 40-43.
  26. Stoeckel S, Brotons J, Mercier J-L (2002). Stratégies de reproduction chez Cardiocondyla elegans : possibilités de transfert inter-nids de sexués. Actes Coll. Insectes Sociaux, 15, p.216.
  27. Stoeckel S & Mercier J-L (2001). Maculinea alcon (Lepidoptera, Lycaenidae) en Brenne : Analyse des relations entre la plante hôte Gentiana pneumonanthe et la fourmi Myrmica scabrinodis (Hymenoptera, Formicidae). Symbioses, 4, 11-18.
Stoeckel S, Gattepaille L, Sjödin P, Schlebusch C, Lascoux M, Jakobsson M.

Integrating knowledge on genomic structure and ancestral diversity to detect outlying genomic regions.10/12/2013, Stochastic Models in Ecology, Evolution and Genetics, Angers, France.



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