PhD : Dynamics of OsHV-1: phylogeographic & modeling approaches for management strategies (M/F)

Deadline for applications : 26/05/2024

Presentation of the research unit or laboratory

The Marine Invertebrate Health Adaptation Unit (ASIM) conducts projects related to i) the study of diseases affecting marine mollusks; ii) the detection and study of disease outbreaks; iii) host adaptation to these diseases (resistance development and associated determinism).

The ASIM unit serves as a strong integration point between research activities and surveillance/reference functions, thanks to its internationally recognized expertise. It is both a National Reference Laboratory (NRL) and a European Union Reference Laboratory (EURL) for marine mollusk diseases. The main objectives of the ASIM unit are to enhance knowledge and data on the genomes of marine invertebrates and their pathogenic microorganisms, to better understand the evolutionary and adaptive mechanisms of marine invertebrates and associated pathogenic microorganisms in their ecosystem, and to develop risk analysis approaches within a broader "One Health" framework. 

Summary

The PhD position is funded by the French Research Agency through a project named IDEAL. The successful applicant will work on disentangling the relative effects of environmental, climatic and anthropogenic factors on the distribution and spread of the Ostreid Herpesvirus Type 1 (OsHV-1).

He/she will use phylogeographic approaches to i) reconstruct OsHV-1 dispersal history over the last decades along the French coast, ii) estimate pathogen transition rates between production areas and iii) identify influencing factors of OsHV-1 lineages dispersal.

Then, he/she will use both reconstructed transmission histories and mathematical dynamic models reflecting transmission dynamics of OsHV-1, to evaluate the expected impact of several potential interventions and provide a decision support tool to stakeholders. To reach this goal, the PhD student will need i) to obtain a spatialised mechanistic model of OsHV-1, ii) to investigate the impact of potential mitigation measures and iii) to use this to develop and disseminate a decision support tool, which will be made available on a web platform.

Key words

Molecular epidemiology, phylodynamics, evolution, infectious diseases, landscape phylogeography, mathematical modeling, spatial epidemiology, bio-informatics, programming

Profil recherché

Candidates will have a master degree in relevant field (Genetics, evolution, spatial or molecular epidemiology, computational biology, bio-informatics)

Knowledge, skills and abilities

- Knowledge of spatial and molecular epidemiology

- Proficiency in bio-statistical tools and programming languages (R, Python, Linux shell)

- Proficiency in concepts and tools for characterizing genomic diversity and spatiotemporal evolution of pathogenic organisms

- Understanding of various molecular genotyping and high-throughput sequencing approaches and their potential applications in population health research

- Familiarity with pathogenic organisms in invertebrates appreciated

- English language proficiency

- Strong writing abilities

Human qualities

- Autonomy and rigor

- Curiosity

- Ability to work in a team

- Synthesis skills

Informations utiles

• LOCALISATION La Tremblade - 17, France - zone de déplacement : internationale
• CONTRAT CDD - 3 ans
• SALAIRE Non défini
• NIVEAU DE QUALIFICATION Ingénieur/Cadre/Bac +5
• EXPÉRIENCE - 1 an
• MODALITÉS DE TRAVAIL Temps complet
• FONCTION Ingénierie - Chimie/Pharmacie/Bio., Bureau d'Etudes/R&D/BTP archi/conception
• SECTEUR Secteur Energie/Environnement
• TÉLÉTRAVAIL Pas de télétravail

Specific working conditions

The successful applicant will be supervised by the coordinator of the project Maude Jacquot, researcher in molecular epidemiology, and Isabelle Arzul, the head of head of the lab (IFREMER, ASIM), and will be working closely with project collaborators at IFREMER (units ASIM, PHYTNESS, SeBiMER).

The successful applicant will also interact with non-Ifremer partners including Simon Dellicour from the Spatial Epidemiology Lab (SpELL) hosted at the University of Brussels (ULB, Belgium), who is an expert on methodological developments and applications in landscape phylogeography. 

He/she will receive a transdisciplinary training by acquiring a wide range of technical skills in a broad range of disciplines (i.e., molecular epidemiology, landscape phylogeography, mathematical modelling, spatial epidemiology, programming) and by interacting with the different partners, leading experts in their field of research. He/she will actively participate to the different dissemination activities and will be encouraged to attend international conferences. 

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 gross for a period of 3 years, which cannot be combined with other scholarships. 

How to apply for this position

Your application files must include:

• a curriculum vitae 
• a cover 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.

The deadline for applications is May 26th , 2024. Nevertheless, we strongly urge you to let us know as soon as possible of your intention to apply, by contacting the subject supervisor: Maude Jacquot

Doctoral students' contracts will start as of October 1st, 2024, subject to the submission of administrative documents authorizing Ifremer to recruit the doctoral student (certificate of completion of the Master 2 or engineering degree + visa for foreign doctoral students outside the EU).

Qui sommes nous ?

IFREMER1625, Route de Sainte Anne • 29280 Plouzané • France

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.