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Open position for a Post-doctoral researcher in Population Genomics: Experimental evolution and the dynamics of adaptation and genome evolution in fungal populations

ABG-120328 Job Any
2024-02-15 Fixed-term 18 Month > €25,000 and < €35,000 annual gross
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Institut national de recherche pour l'agriculture, l'alimentation, l'environnement (INRAE)
- Ile-de-France - France
Agronomy, agri food
  • Biology
population genomics, fungi, antifungals, adaptation, population dynamics
2023-04-15
Research and Development

Employer

INRAE is a French public research institution that focuses on issues related to agriculture, food and food security, environment and land management, with a particular emphasis on sustainable development. It gathers a working community of around 12,000 people, including more than 200 research units and 42 experimental units located throughout France. The Plant Health Department (SPE) deals with issues relating to crop health in the broadest sense of the term, including protection against pests and diseases but also making the most of beneficial interactions with micro-organisms, maintaining the pollination service and analysing the consequences of health protection in terms of its impact on natural populations.

The BIOGER research unit (about 40 scientists) works on major fungal crop pathogens using pluri-disciplinary strategies from functional genomics, evolution and population genetics to microbiology, epidemiology and modelling. You will be welcomed in a multidisciplinary team of 6 scientists and engineers, dealing with the adaptation of fungi to multiple selection pressures and will collaborate with the bioinformatics platform at INRAE BIOGER.

https://bioger.versailles-grignon.hub.inrae.fr/

By joining our team, you will benefit from :

- an interdisciplinary working environment within a research unit that conducts internationally recognised research in the field of plant pathology,
- an environment of scientific excellence as part of the Université Paris Saclay, of which INRAE is a partner  
- a location in Palaiseau (78, Île-de-France), on a site that accommodates around 2,000 students and 1,350 teacher-researchers, researchers, technicians and administrative staff from AgroParisTech and INRAE, on the same campus. The location has a subsidised catering service for lunches
- INRAE's commitment to social and environmental responsibility (RSE),

- 25 days' holiday + 15 days' leave per year
- the possibility of teleworking up to three days a week
- access to sporting and cultural activities (sports grounds and parks nearby)
- 50% reimbursement of travel costs, with easy access to the site by public transport
- a Sustainable Mobility package if you use a personal bicycle or car-pool to commute to and from work
- a skills development scheme: training, career guidance, etc.
- social support: advice and listening, social assistance and loans
- a range of holiday and leisure services: holiday vouchers, discounted accommodation, etc.
- support for parenthood: CESU childcare, leisure services, etc.

Position and assignments

Understanding how adaptive traits arise, spread and persist within populations over time is a key question in evolutionary biology. In pathogens, adaptation to antifungals constitutes a textbook example of evolutionary rescue that can easily be (re)produced in the lab and that compromises crop health as well as it can worsen the environmental impact of the chemicals used. However, field evidence suggests that adaptive trajectories are complex and difficult to predict.

We are looking for a highly motivated post-doctoral scientist to understand the dynamics of adaptation to antifungals in the populations of the model ascomycete Zymoseptoria tritici, responsible for septoria leaf blotch disease on wheat. As a proof of concept, we propose to disentangle the respective impact of selection components first in a simplified environment and over a compressed timescale. Therefore, you will acquire whole genome resequencing data to quantify genomic changes having occurred during experimental evolution, from samples already available in the lab. Samples include populations and pure isolates having undergone constant or fluctuating selection from distinct antifungals. You will use the variation in the frequency of polymorphisms over generations to visualize the dynamics of adaptation, understand the main drivers of adaptation and calculate the rate of adaptation, depending on the environment. The results will provide a conceptual framework for understanding in further work how fungi may evolve in response to solo or joint selective pressures occurring in field agroecosystems.

Related references

Ballu, A., et al. (2023). "Antifungal alternation can be beneficial for durability but at the cost of generalist resistance." Communications Biology 6(1): 180.

Feurtey, A., et al. (2023). "A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen." Nature Communications 14(1): 1059.

Geographic mobility:

European

Telework

Full time
max 3 jours par semaine

Starting date

2024-04-01

Profile

  • PhD degree in population genomics, evolutionary biology or similar subject relevant for the project, obtained not earlier than 3 years before the start of this project;
  • An excellent knowledge on statistics applied to life sciences and statistical tools, such as R;
  • Knowledge in evolutionary biology, including theoretical aspects of adaptation. Interest in plant pathology and crop protection will be appreciated;
  • A demonstrated capacity for team work and supervision of students and/or technical staff;
  • A proven ability to communicate research results through scientific publications or oral presentations;
  • Proficiency in English is compulsory, knowledge of French would be appreciated.

Goals

You will be responsible for :

   - ensuring the (re)sequencing of experimental evolutionary lines of Z. tritici relevant to your research question, in interaction with a service provider and in collaboration with the team's scientists and in connection with ongoing projects ;
   - designing and implementing bioinformatics analysis scripts to characterise the adaptive dynamics in the genomes of the different lineages; calculating the rates of adaptation in different environments and analysig how the diversity of selection pressure modulates adaptation at genome level;
    -contributing to the exploitation of these results through publications and conference presentations.

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