PhD Engineer CNRS
Laboratoire Ecologie et Evolution (UMR7625)
Equipe Eco-Evolution Mathématique
Ecole normale supérieure 46 rue d’Ulm
75005 PARIS FRANCE
+33 1 44 32 23 10
|Choose your topic…|
RESEARCH INTERESTS :
Combine theoretical and experimental approaches
Ecology & Evolution :
This approach can be seen as the study of evolution that incorporates an understanding of the interactions between organisms and their environment.
Environment is also other organisms (biotic interactions). I’m interested on the evolution of biotic interactions like cooperation, predator-prey and host-parasite interactions, symbiosis.
Population genetics : experimental and theoretical evolution
Biological model : Escherichia coli (on left) and Dyctyostelium discoideum (on right)
Population genetics is the study of the allele frequency distribution and change under the influence of the four evolutionary forces: natural selection, genetic drift, mutation (and gene flow.)
Our experimental system is an evolving bacterial and amoeba population stained with neutral fluorescent markers to follow allele frequency.
The stochastic model is based on classic Wright-Fisher model.
Modern computational approach in poplation genetics :
It’s possible to develop models that start to approach the effective population size :
Maximum likelihood :
Likelihood is the probability of data set given that the model for those data is deemed to be correct (Fisher 1934). The likelihood principle says that a model (with parameters values) is more likely than another if it’s the one for which data are more probable.
Baeysian analysis :
Bayesian approach is based on likelihood. Bayesian includes a second element : the prior density for parameters. The prior makes it possible to calculate a posterior parameter density.
interacting populations and population dynamic
Dictyostelium discoideum is an amoeba. When food is available, they take the form of individual amoeba. When food is exhausted, they cooperate to form a multicellular assembly called slug.
D.discoideum aggregation :
Several theories like kin selection, reciprocity, tragedy of the commons help to explain why natural selection favors some types of cooperative behaviors.
Jeon K.(1987) showed that free-living amoeba became dependant on bacterial endosymbionts which had infected the amoeba initially as intracellular parasites.
Recent works of Todoriki (2002, 2006, 2008) showed the ‘change in physiological state of E.coli cells at the initial stage for establishing a new endosymbiotic relationship with D.discoideum cells’.
How did these changes occur?
PhD SUBJECT (since October 2007):
BIOTIC NATURAL SELECTION AND GENETIC DRIFT EFFECTS ON POLYMORPHISM
Theoretical and experimental evolution
Supervisors: Frantz Depaulis and Minus Van Baalen
Erick Denamur, director of the Laboratory Ecology and evolution of microorganisms, INSERM U722, Xavier Bichat Medical school PARIS
and Clément Nizak, Research scientist, laboratory physics spectrometry CNRS UMR5588 BIOP GRENOBLE.
The experimental system follows evolving bacterial and amoeba populations, either alone or in interaction: the ecological interaction produces selection, drift results from periodic bottlenecks (serial transfer).
The stochastic model mimics our experimental design and is based on classic Wright-Fisher model, adding overlapping generation, fluctuating selection, mutation, bottleneck to characterize molecular evolution.
What are the contributions of selection and drift on allele frequency variations?
Which factors are responsible of differences between census population size and effective size?
Are selective coefficients fluctuating in time?
OTHER RESEARCH PROJECT :
Works in collaboration with Erick Denamur, director of the Laboratory Ecology and evolution of microorganisms, INSERM U722, Xavier Bichat Medical school PARIS
Interspecific relationships between different E.coli strains and D.discoideum :
- Population dynamic :
How interact D.discoideum with different E.coli strains which have different characteristics (toxin, different virulence, encapsulated or not..) :
- Interactions Coli-Dicty
- Population dynamic :
- Towards symbiosis :
Repeat Todoriki’s experiments with different E.coli strains
Different E.coli strains virulence on D.discoideum:
We have 21 pathogens, 11 commensals and 3 laboratories E.coli strains. Pathogen strains are well described with their different virulence factors and have been studied with mouse and worm. We want to study these different strains with our model D.discoideum.
- Towards symbiosis : Repeat Todoriki’s experiments with different E.coli strains
COMMUNICATIONS AND PUBLICATIONS :
Experimental evolution of local adaptation in a microbial host-parasite system, Sandrine Adiba, Michèle Huet, Oliver Kaltz. Roscoff , Sept 2007, Poster
Selection and drift in interacting polymorphic populations, Sandrine Adiba, Minus van Baalen, Frantz Depaulis, Sèvres, April 2008, Poster
Experimental evolution of local parasite maladaptation, Sandrine Adiba, Michèle Huet, Oliver Kaltz, JEB, 2010.
From grazing resistance to pathogenesis: the coincidental evolution of virulence factors, Sandrine Adiba, Clément Nizak, Minus van Baalen, Erick Denamur, Frantz Depaulis, PlosOne, 2010.
Natural selection and genetic drift effects on neutral polymorphism, Sandrine Adiba, Lambert Edition, 2011.
Soon in english…
FREE PROGRAMS WITH ’R’ :
Statistical analysis :
Available soon :
- Anova with repeated measures
- Linear regression
- Logistic regression
Theoretical model analysis