Graduate position: Theoretical population genetics and evolution
From the Evolution Directory (EvolDir) via Twitter.
Rennes University, France and the French National Institute for
Agricultural research invite applications for a full-funded
postgraduate PhD position in
POPULATION GENETICS AND EVOLUTION OF PARTIAL ASEXUALITY: INFERRING AND
MODELLING THE IMPACTS OF PARTIAL ASEXUALITY ON POPULATION GENOMICS
At the Joint Research Unit "Institute of Genetic, Environment and
Plant Protection".
Application before the 11th June 2012 (12 o'clock, French time).
Please contact solenn.stoeckel@rennes.inra.fr and
jean-christophe.simon@rennes.inra.fr
http://www.vas.univ-rennes1.fr/en/
Socio-economic and scientific context
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The sudden advances of molecular biology in the last thirty years
allowed biologists to extensively test, successfully use and improve
the conceptual framework of population genetics. Regarding partially
asexual species, population genetics allowed biologists to
qualitatively identify some sexual or asexual events within
populations and to disentangle sexual from asexual lines using
empirical criteria. However, because of the lack of adapted
theoretical model, biologists cannot compare the observed evolutionary
patterns of these species to theoretical referential predictions, as
they commonly do to study the ecology and the evolution of sexual
species. We cannot content on current methods as they mainly rely on
qualitative expertise. We are developing adapted models that take into
account for the specific genetic functioning of such species. These
models will enable non-biased predictions and reliable biological
inference methods from field genetic data.
Assomptions and questions
~~~~~~~~~~~~~~~~~~~~~~~
Questions prompting this project are 1) what are the quantitative
effects of partial asexuality on the expected gen-etic/-omic diversity
and its structure in metapopulations when those ones undergo selective
pressures? and 2) Do the joint effects of the evolutionary forces and
this mating mode result in distinctive genomic patterns from which
biologists may infer the current and past evolution of such species?
The PhD student will answer by completing a population genetics model
dedicated to partially asexual organisms so it takes into account for
selective processes. This model will allow to study the evolutionary
specificities and the genomic patterns left by of such functioning,
and to propose some inference methods. Our model without selection has
already shown that evolution of partially asexual species diverges
from pure sexual and asexual species.
The main steps of the thesis
~~~~~~~~~~~~~~~~~~~~~~~
The work will consist in extending a mathematical model by formalizing
the selective processes applied on genotypes. This step will complete
the integration of all evolutionary processes in a population genetics
model adapted to partially asexual species that has been developed
with the appropriate formalism. The model will be included in
optimized computation algorithms (coll. Symbiosis team, IRISA,
Rennes). The model outputs will be analysed and confronted to
simulation results, biological knowledge and experimental data already
obtained by the host team, the partners of the ANR (the collaborative
grant that fund the PhD expenses) and a scientific network. Then, the
PhD student will explore the trends of his quantitative predictions,
identify the characteristic effects of partial asexuality on
population genetics indices under selection and participate in
providing new descriptive indices adapted to such species (Coll.
S.Arnaud-Haond, Ifremer, Brest ). He will participate in the
development of quantitative inference methods to identify forces and
effective rates of asexuality under which genomes have evolved.
Finally, the PhD student will reinterpret the historical significance
of asexuality in the evolutionary histories of varied organisms.
According to the student interests, our lab performs global surveys of
some partially asexual species of aphids and whole genome functional
and evolutionary analyses. If interested, the PhD student will have
the opportunity to collaborate to these others works to open up on
field, bioinformatics and lab works.
Methodological and technical approaches considered
(~15%) Running and developing mathematical population genetics models
(Markov chain, differential equation, diffusion process, network
analyses, sensitivity analysis) and simulations.
(~15%) Low level parallel computation, optimized compilation, GPGPU.
(~70%) Analyses and interpretations of theoretical predictions in
population genomics and of already acquired datasets.
Scientific and technical skills required by the candidate
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Good knowledge in at least one of those domains and motivated
interests to learn the others: a) Mathematical modelling (Markov
chain, stochastic differential equation); b) optimized algorithm and
computation (python, C, GPGPU, cloud computing); c) Population
genetics and evolution.
---------------------------------------------------------------------------------------------------------------
Pragmatic context and objectives of the PhD
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This PhD position forms a part of a new ambitious project entitling
Revisiting the Population Genetics and Genomics of clonal organisms
funded by the French National Research Agency for the next 4 years. It
will involve 4 other repute French teams and will imply collaboration
outside of the French country. The student will visit their labs
yearly using the funds already allocated for and we will encourage the
student to build his/her own collaborations. The PhD student will be
supervised by Solenn Stoeckel and Jean-Christophe Simon. We have the
will to adopt a trans-disciplinary approach based on our local weekly
collaboration with the INRIA (French Institute of Computational
Sciences) and the support of Pr. JP Masson from Agrocampus Ouest (on
Mathematics and Statistics).
At the end of the PhD, the student will be able to commonly use
mathematics and computation to develop models to perform massive and
synthetic data analyses from genomic data to understand and infer
complex evolutionary processes occurring on populations and species.
We target to publish papers in journals as BioInformatics, Genetics,
Heredity, Molecular Ecology and Trends in Evolution and Ecology.
*Salary and appointment*: The duration of the PhD training period is
three full years. The successful candidate will receive a postgraduate
fellowship of 1429.00 € per month including French public welfare
system. Some social benefits in addition can be obtained (e.g. housing
and family benefits).
Environment of the thesis
Rennes is a strong place in France to study ecology and evolution. The
city welcomes 60.000 university students per year. The graduate school
V.A.S. (Vie-Life, Agronomie-Agronomy, Santé-Health) regroups 60
research teams (640 researchers) and 320 doctoral students. Ninety
doctoral degrees are awarded annually in this fundamental biology,
agronomy and health graduate school. One year after the degree, 90% of
the PhD have a job and 65% find a tenured or secured position. It
offers a creative and stimulating environment through seminars,
courses and places to interact with other researchers and students.
The city: More than 300000 inhabitants of whom a fifth of students.
Situated near the Atlantic ocean, it is surrounded by lovely forest
and natural countryside that inspired lots of Celtic tales as the
Knights of the Round Table. It's a city famous for its cultural
activities (a national theatre, many music places and festivals, art
and sciences museums, gastronomy, number of living and repute pubs)
with great accessibility for students. The city is served by a
important fast-railway station (every hour departure to Paris,
situated at 2 hours ~70€) and an airport. You can easily move into the
countryside and at the sea by bus and train (for windsurfing, sailing,
diving,...). The cost of life is quite inexpensive (monthly cost of
2-rooms flat~450€, monthly transport subscription ~30€, unlimited
internet and international phone ~35€, unlimited 3G phone
subscription~25€).
---------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------
Some selected publications from the supervisors of the PhD:
---------------------------------------------------------------------------
- Ollivier, M., T. Gabaldon, J. Poulain, F. Gavory, N. Leterme, J. P.
Gauthier, F. Legeai, D. Tagu, *J. C. Simon*, and C. Rispe. 2012.
Comparison of gene repertoires and patterns of evolutionary rates in
eight Aphid species that differ by reproductive mode. GENOME BIOLOGY
AND EVOLUTION 4:155-167.
- *Stoeckel, S.*, E. K. Klein, S. Oddou-Muratorio, B. Musch, and S.
Mariette. 2012. Microevolution of S-allele frequencies in wild cherry
populations: respective impacts of negative frequency dependent
selection and genetic drift. EVOLUTION 66:486-504.
- Tsuchida, T., R. Koga, M. Horikawa, T. Tsunoda, T. Maoka, S.
Matsumoto, *J.-C. Simon*, and T. Fukatsu. 2010. Symbiotic Bacterium
Modifies Aphid Body Color. SCIENCE 330: :1102-1104.
- Navascués M, *Stoeckel S*, Mariette S 2010 Genetic diversity and
fitness in small populations of partially asexual, self-incompatible
plants. HEREDITY 104(5):482-492
- *Simon J.C.*, *Stoeckel S.* & Tagu D. 2010. Evolutionary and
functional insights into reproductive strategies of aphids. COMPTES
RENDUS BIOLOGIES 333(6-7):488-496.
- Jaquiery, J., *S. Stoeckel*, C. Rispe, L. Mieuzet, F. Legeai, and
*J.-C. Simon*. 2012. Accelerated Evolution of Sex Chromosomes in
Aphids, an X0 System. MOLECULAR BIOLOGY AND EVOLUTION 29:837-847.
1102-1104.
- Peccoud, J., A. Ollivier, M. Plantegenest, and *J.-C. Simon*. 2009.
A continuum of genetic divergence from sympatric host races to species
in the pea aphid complex. PROCEEDINGS OF THE NATIONAL ACADEMY OF
SCIENCES OF THE UNITED STATES OF AMERICA 106:7495-7500.
- Nespolo RF, Halkett F, Figueroa CC, Plantegenest M, *Simon J-C* 2009
Evolution of Trade-Offs between Sexual and Asexual Phases and the Role
of Reproductive Plasticity in the Genetic Architecture of Aphid Life
Histories. EVOLUTION 63, 2402-2412.
- Gilabert A., *Simon J.C.*, Mieuzet L., Halkett F., *Stoeckel S.*,
Plantegenest M. & Dedryver C.A. 2009. Climate and agricultural context
shape reproductive mode variation in an aphid crop pest. MOLECULAR
ECOLOGY 18(14):3050-3061.
- Peccoud, J., C. C. Figueroa, A. X. Silva, C. C. Ramirez, L. Mieuzet,
J. Bonhomme, *S. Stoeckel*, M. Plantegenest, and *J. C. Simon*. 2008.
Host range expansion of an introduced insect pest through multiple
colonizations of specialized clones. MOLECULAR ECOLOGY 17:4608-4618.
- *Stoeckel S*, Grange J, Fernandez-Manjarres JF, et al. 2006
Heterozygote excess in a self-incompatible and partially clonal forest
tree species - Prunus avium L. MOLECULAR ECOLOGY 15, 2109-2118.
- Halkett F., *Simon J.C.*, Balloux F. 2005. Tackling the population
genetics of clonal and partially clonal organisms. TRENDS IN ECOLOGY
AND EVOLUTION. 20(4), 194-201.
contacts:
--------
Jean-Christophe Simon and Solenn Stoeckel
UMR 1349 IGEPP INRA - Agrocampus Ouest Rennes - Université Rennes 1
Domaine de la Motte, BP35327
F-35653 Le Rheu cedex, France
Phone: +33 (0)2 23 48 51 54
Fax: +33 (0)2 23 48 51 50
jean-christophe.simon@rennes.inra.fr
Solenn Stoeckel, currently visiting at Uppsala University until June 2012
Dept. of Evolutionary biology, EBC, Mattias Jakobsson lab,
Uppsala University, room 1056
Norbyägen 18D,
75236 Uppsala, Sweden
solenn.stoeckel@rennes.inra.fr