Job title : PhD : Modelling environmental DNA to derive abundance indices (M/F); The Institute and the recruiting department:
A pioneer in ocean science, IFREMER’s cutting-edge research is grounded in sustainable development and open science. Our vision is to advance science, expertise and innovation to:
- Protect and restore the ocean
- Sustainably use marine resources to benefit society
- Create and share ocean data, information & knowledge.
With more than 1,500 personnel spread along the French coastline in more than 20 sites, the Institute explores the 3 great oceans: the Indian, Atlantic and Pacific oceans. A leader in ocean science, IFREMER is managing the French Oceanographic Fleet and its dedicated scientists create ground-breaking technology to push the boundaries of ocean exploration and knowledge, from the abyss to the atmosphere-ocean interface.
Well-established in the international scientific community, our scientists, engineers and technicians are committed to advance knowledge about our planet’s last unexplored frontiers. They provide the science we need for informed decision-making and public policy and they transfer this knowledge and technology to businesses to fulfill public and private needs.
Core to our mission is also to strengthen public awareness about the importance of understanding the ocean and its resources, and empowering future generations of leaders through education and outreach national campaigns.
Founded in 1984, IFREMER is a French public organization and its budget approximates 240 million euros. It is operating under the joint authority of the French Ministry for Higher Education, Research and Innovation, the french Ministry of the Sea, the French Ministry for the Ecological and Solidary Transition, and the French Ministry of Agriculture and Food.
General areas of responsibility
The joint research unit (UMR) “Dynamics and Sustainability of Ecosystems: from the Source to the Ocean” (DECOD) brings together researchers, engineers and technicians from Ifremer, INRAe and Institut Agro Rennes-Angers with laboratories in Brest, Lorient, Nantes and Rennes. DECOD’s activities focus on the analysis of ecological and evolutionary processes at work in aquatic environments and their interfaces, from the source to the ocean, on the assessment of the state of ecosystems, and on the construction of scenarios for these ecosystems.
To address these issues, the Ecology and Models for Fisheries (EMH) laboratory acquires knowledge on marine ecosystems and implements models and quantitative approaches based on empirical data, in the context of an ecosystem approach to fisheries management.
Methods for assessing fish stocks require significant resources to provide reliable abundance estimates, but do not allow the assessment of rarer species. To fill this gap, a new methodology seems promising, the analysis of abundance by environmental DNA (eDNA). However, statistical models for using eDNA observations for estimating abundance indices accounting for the drift and degradation of eDNA et making use of other available information (habitats, catches) still need to be developed and tested for the marine environment.
The objectives of the thesis are to:
i) develop a diffusion-advection model of DNA molecules accounting for the degradation of DNA as a function of temperature and the hydrology of the study area using an individual-based model coupled with a hydrodynamic model (e.g. CROCO); ii) develop a spatial state-space model with a latent layer for abundance and several observation models which includes the results from the diffusion-advection model and the molecular analysis processes for eDNA data; iii) apply the models to available eDNA and trawl fish data from the Bay of Biscay.
eDNA, Lagrangian transport modelling, exploited species, state-space model, fish.
Required Knowledge, skills, and characteristics
Master of Science in marine ecology with strong competence in mechanistic and statistical modelling. The applicant needs to be able to work as a part of a team. Good practice in R/C, C++ or Matlab, good communication skills and good spoken and written English are required.
Specific working conditions
- Occasional work at sea
- Occasional travel in France and abroad
A Phd is a real opportunity to work on Ifremer’s scientific and technological priority themes. It entitles the holder to a gross monthly salary of 2300 euros for a period of 3 years, which cannot be combined with other scholarships.
How to apply for this position?
Your application file must include:
- a curriculum vitae
- a covering letter
- a reference letter
- an academic transcript (Bachelor + Master 1 and first semester Master 2)
Your application must be compiled into 2 PDF files, up to 3 MB for each file:
In case of any problems attaching your documents, please upload your CV on this page (this step is mandatory for your application to be considered) and send all documents to the thesis supervisor: firstname.lastname@example.org
The deadline for applications is April 23rd, 2023. Nevertheless, we strongly urge you to let us know as soon as possible of your intention to apply, by contacting the subject supervisor. In parallel, please submit your application to the doctoral school: https://ed-sml.doctorat-bretagne.fr/en
Doctoral students’ contracts will start as of October 2nd, 2023, subject to the submission of administrative documents authorizing Ifremer to recruit the doctoral student (certificate of completion of the Master or engineering degree + visa for foreign doctoral students outside the EU).
How to apply for this position:
Deadline for applications: 23/04/2023; All applications are processed exclusively via our website. Interested candidates can apply by clicking the “Apply” button.