Postdoctoral position OT-26099
PhD position in A phylogenetic approach to characterize the unknown diversity of aquatic environments
VILLEURBANNE 69100
INRAE presentation
The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.
Work environment, missions and activities
You will be based in Villeurbanne within the EcoFlowS team (https://ecoflows.inrae.fr/) in the RiverLy research unit (INRAE, https://riverly.inrae.fr/) in partnership with the Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA, UMR 5023 Université Claude Bernard Lyon 1 - CNRS - ENTPE, https://umr5023.univ-lyon1.fr/) as part of a postdoctoral research position within the ALIQUOT project (ANR-22-PEPR-0011).
This position aligns with the objectives of the ALIQUOT project, laureate in 2023 of the 1st call for proposals of the National Exploratory Research Program OneWater - Water as a Common Good. Launched in March 2022, this program financed by the France 2030 plan (€53M) aims to develop knowledge in water sciences to change the paradigm and rehabilitate water as a common good.
The ALIQUOT project aims to get a better understanding of the dynamics of environmental nucleic acids (DNA/RNA) in aquatic environments, so that they can be used as sentinels of the diversity and functioning of socio-hydrosystems. The project brings together a national consortium of ten laboratories from CNRS, BRGM, Sorbonne Université and INRAE involving several PhDs and post-doctorates in a collaborative environment. One of ALIQUOT's tasks is to develop an innovative approach to molecular monitoring of biodiversity in orphaned aquatic environments (e.g. groundwater), for which genetic reference databases are largely incomplete, making reliable taxonomic assignments impossible for many taxonomic groups.
In this context, we are offering a two-year postdoctoral research position focusing on the development of a bioinformatics approach aimed at characterizing unknown (i.e., undescribed) diversity through the phylogenetic placement of high-throughput sequencing data on reference trees derived from mitogenome sequencing.
The first step will be to reconstruct a reference metazoan phylogenetic tree from mitogenome data. Then, a mitogenomic approach will be used to reconstruct complete mitogenomes from DNA extracted directly from the pool of species collected in situ (« bulk »). These data will be used to reconstruct evolutionary relationships between the collected organisms, and to include them in the broader reference phylogenies constructed previously.
Secondly, the use of phylogenetic placement algorithms will enable to place the mitochondrial “DNA barcodes” routinely used by metabarcoding approaches to characterize animal biodiversity in the metazoan phylogenetic tree. This bridge between metabarcoding data and evolutionary data (mitogenomes) will make it possible to monitor biodiversity in environments for which reference databases are absent (or largely incomplete), and will be compatible with an approach of species retro-identification when they are formally described.
The aim of this post-doctoral position is to develop a proof of concept for such a method. The person recruited will be responsible for:
1. Set up an automated phylogenetic reconstruction approach for metazoans based on open-access mitogenome data (NCBI).
2. Analyze from a bioinformatics point of view the results of a study on controlled communities to test the feasibility of reconstructing complete mitogenomes from DNA extracted from a pool of individuals belonging to species with different phylogenetic proximities.
3. Carry out an initial study using data from macro-invertebrates collected in situ (“Bulk” and eDNA), in order to test the approach under real-life conditions.
4. Work in collaboration with two research engineers, in molecular biology for data production and in bioinformatics for data management and archiving.
5. Participate in the molecular biology work related to this task and contribute to the animation of the project.
Special conditions of activity: All or part of the laboratory work will be carried out at LEHNA (500m away from RiverLy), and frequent meetings will be hold with LEHNA colleagues and, more generally, with members of the ALIQUOT project. The candidate will have access to the PRABI AMSB computing cluster, the IT platform of the BioEEnViS Research Federation (http://amsb.prabi.fr/opendata.html). Working remotely will be possible up to a maximum of 3 days/week. The position is located in a sector covered by the protection of scientific and technical potential (PPST), and therefore requires, in accordance with regulations, that the candidate be authorized by the competent MESR authority.
Training and skills
Recommended training: PhD in bioinformatics related to biodiversity sciences or in phylogeny/phylogenomics or environmental genomics.
Desired knowledge: Good knowledge in molecular ecology, phylogeny/phylogenomics and environmental genomics. Knowledge of statistical analysis of biodiversity, as well as practical knowledge of molecular biology will be appreciated.
Appreciated experience: Experience in programming and bioinformatics for analytical pipelines, in particular de novo genomic reconstruction, phylogenetic/phylogenomic analysis and analysis of NGS metabarcoding data. Experience in aquatic biodiversity and/or statistical analysis for community ecology would be appreciated, but is not mandatory.
Skills: Good writing and oral communication skills. Good interpersonal skills, teamwork, autonomy and organizational skills. Curiosity and good command of written and spoken English.
INRAE's life quality
By joining our teams, you benefit from (depending on the type of contract and its duration):
- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.
How to apply
Send a covering letter by email or postmail, a short research project you are considering (1 page maximum) and a CV including your publication list and a contact of two referees.
David Eme, INRAE/RIVERLY-Ecoflows 5 rue de la Doua, 69100 Villeurbanne
Tristan Lefébure et Johan Pansu, LEHNA UMR 5023, Université Claude Bernard Lyon 1, 3-6 rue Raphael Dubois, 69100 Villeurbanne.
All persons employed by or hosted at INRAE, a public research establishment, are subject to the Civil Service Code, particularly with regard to the obligation of neutrality and respect for the principle of secularism. In carrying out their functions, whether or not they are in contact with the public, they must not express their religious, philosophical or political convictions through their behaviour or by what they wear. > Find out more: fonction publique.gouv.fr website (in French)