Phd Genetic Connectivity Between Anthropogenic Marine Structures And Natural Habitats In Mussels And Cionas M - F H/F - Ifremer

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www.ifremer.frClosure date for receipt of applications : 17/06/2025

The ASIM unit (Marine Invertebrate Health and Adaptation, https://asim.ifremer.fr/Presentation), based at the Ifremer station in La Tremblade, focuses on the health of species of interest in marine aquaculture, with a particular emphasis on bivalve molluscs. The ASIM unit is developing recognized expertise in the interactions between these species and their associated pathogenic organisms, as well as in the genetic basis of the adaptive responses implemented in an open, constantly changing environment. Its work focuses on three main areas : 1) describing the diversity of marine invertebrates and pathogenic microorganisms; 2) understanding the interactions between invertebrates, pathogens and environmental factors; 3) anticipating the emergence of new diseases or innovative forms of marine invertebrates.

Summary

This PhD thesis is part of the GreyCo project (Grey Connectivity, 2024-2028). This project aims to gain a better understanding of the "grey connectivity" between artificial structures, in a context of increasing marine urbanization, marked by the development of ports, mussel farming areas and offshore wind farms (https://asim.ifremer.fr/Projets/Projets-en-cours/GREYCO-2024-2028).

The main objective of this thesis is to evaluate the genetic dynamics linked to the anthropization of marine environments, particularly in terms of genetic connectivity, for two benthic species complexes emblematic of the colonization of artificial substrates : marine mussels (Mytilus edulis and M. galloprovincialis) and ascidians (Ciona robusta and C. intestinalis).

The central issue is how these new artificial structures modify gene flows between populations : do they facilitate the meeting of previously isolated lineages? Do they create relay habitats for the dispersal of individuals between ports, buoys, wind turbines and natural environments (foreshore)? To answer these questions, samples will BE collected from different types of sites (anthropized and natural), then genotyped using three complementary approaches : genotyping of around ten diagnostic SNP markers using the KASP method on all the individuals sampled, 60K SNP genotyping chips on a sub-sample, and finally sequencing of a few complete genomes phased using the haplotagging technique on the most informative individuals, thus covering a gradient of increasing resolution in terms of molecular markers.

After bioinformatics processing, the data will BE used to identify lineages and/or the origin of individuals, and to reconstruct evolutionary trajectories based on genetic profiles (hybridization, admixture, introgression). Population genetics analyses (genetic diversity and differentiation indices, PCA, STRUCTURE, genomic differentiation scans, hybrid detection, ancestry inferences, etc.) will BE used to assess connectivity between different habitats and identify potential dispersal corridors created by new artificial infrastructures.

Key words

Genetic connectivity, grey connectivity, anthropogenic structures, marine urbanization, offshore wind turbines, gene flow, hybridization, introgression, KASP, haplotagging, genetic diversity, genetic differentiation

Specific working conditions

You will BE supervised by the project coordinator, Florentine Riquet (ASIM-Ifremer), and Nicolas Bierne (CNRS - ISEM), researchers in evolutionary ecology. He/she will work in close collaboration with the GreyCo project partners (ASIM-Ifremer, ISEM-UM, Sebimer-Ifremer, Dyneco-Ifremer, Open-C, ULCO).

You will receive transdisciplinary training, acquiring a wide range of technical skills in numerous disciplines (molecular biology, evolution, ecology, bioinformatics) and interacting with the various partners, renowned experts in their fields of research. He/she will actively participate in various dissemination activities and will BE encouraged to attend international conferences.

Required knowledge, skills and characteristics

Candidates will have a master degree in relevant field(s) (Genetics, Evolution)
- Knowledge, skills and abilities
- Molecular biology : DNA extraction, quantification, knowledge about the different sequencing techniques used
- Bioinformatics and data processing (population genomics)
- Strong writing skills
- Human qualities
- Autonomy and rigor
- Ease of communication
- Curiosity and initiative
- Ability to work in a team
- Synthesis skills