Supervisor(s): Erwan Quéméré (INRAE, Rennes), Marianne Robert (IFREMER, Lorient)
Location: INRAE DECOD, Rennes (https://www.umr-decod.fr/fr)
Duration: 6 months (from January 2027) – Application deadline: 15 September 2026
Summary
Restoring ecological connectivity through dam removal can rapidly transform river ecosystems by reconnecting previously isolated habitats, restoring migratory pathways, and modifying hydrological and habitat conditions. Understanding how fish communities respond to these changes is essential for assessing the ecological outcomes of river restoration. Environmental DNA (eDNA) metabarcoding provides a powerful, non-invasive approach for monitoring fish communities at large spatial and temporal scales, including rare, elusive, and migratory species.
The Sélune River basin provides an exceptional case study of ecological restoration following the removal of two large dams and the restoration of river connectivity in 2022. This major environmental transition has modified hydrological, morphological, and water-quality conditions, creating new environmental opportunities and constraints for fish communities and potentially reshaping their spatial distribution, community composition, and recolonization dynamics.
The internship will investigate the spatio-temporal trajectories of fish communities following dam removal, using a unique long-term eDNA dataset. The main objectives will be to:
(1) Characterize changes in fish communities in terms of taxonomic and functional diversity;
(2) Analyse recolonization trajectories, with a particular focus on migratory species;
(3) Identify the main environmental gradients structuring fish assemblages.
The internship will use a standardized eDNA dataset generated through metabarcoding of a fragment of the mitochondrial 12S rRNA gene to characterize fish communities across the Sélune River basin. Samples were collected between 2021 and 2026 at 33 stations, with two sampling campaigns per year (spring and late summer), providing a unique time series covering both the pre- and post-dam removal periods. The eDNA data are complemented by hydrological, hydromorphological, and physico-chemical data from the Sélune Observatory, including discharge, hydrological connectivity, habitat characteristics, temperature, dissolved oxygen, turbidity, and nutrients. Community ecology and multivariate approaches will be used to identify spatial and temporal patterns in fish assemblages and their relationships with environmental gradients. Functional diversity metrics will complement taxonomic analyses to assess changes in community structure and ecological functioning.
This internship is embedded within a collaborative research effort involving researchers from different sites and institutions of the DECOD research unit, combining expertise in molecular ecology, community ecology, and aquatic ecosystem ecology. In addition to the main supervisors, Alain Danet (INRAE Rennes) and Dorothée Kopp (IFREMER Lorient) will contribute their expertise in functional ecology. The coordination team of the Sélune Observatory, Laura Soisson and Manuel Cheve, will also contribute to the project by providing their expertise on the Sélune River basin and access to available environmental data.
Candidate profile: The candidate should have a strong interest in aquatic and community ecology, with an interest in quantitative approaches and statistical analysis of ecological data. Experience with R, multivariate analyses, and/or functional ecology would be an advantage. Knowledge of eDNA metabarcoding or bioinformatics is welcome but not required, as the sequencing data have already been bioinformatically processed. Rigor, autonomy, analytical skills, and an ability to work in an interdisciplinary team are expected.
Contact : Erwan Quéméré – erwan.quemere@inrae.fr et Marianne Robert – Marianne.Robert@ifremer.fr
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