Research
and goals
Main Current projects
AEROPO (2023-2024)
Attainment of the evolutionary history of genes playing a key role in diadromous fish (AEROPOT): case of a species with commercial and aquatic interests (European eel, Anguilla anguilla). Throughout its range, European eel is the subject of particular attention due to its critically endangered (CR) conservation status (IUCN). Within the framework of the objectives of improving i) the knowledge on these species for a better conservation and ii) the selection processes in aquaculture, we propose within this project to describe the evolution of the history of the genes over time thanks to the DNA from archaeological bones (vertebrae) from partnerships set up during a project supported in 2020-2022 by INRAE (PaleoFish). Particular attention will be paid to genes/gene networks recognized as being crucial in the adaptation of organisms to environmental changes.
To achieve this goal, we will doing the whole genome sequencing of samples from Mesolithic, Neolithic, Protohistory, Antiquity, Medieval, and Late Medieval. It will be the first time that whole genome from ancient DNA in European eels will be realized.
Funding by MIRA – UPPA.
Parternship: Régis DeBruyne (MNHN), Brice Ephrem (CNRS), Sheila Hamilton (Bournemouth University), Philippe Béarez (MNHN), Ulrich Schmölcke (Munich State Zoological Collection), Inge Van der Jagt (Cultural Heritage Agency of the Netherland), Daniel Makowiecki (Institute of Archaeology), Jennifer Harland (Archaeology Institute).
Movie in which I explain how to recognize the type of eel’s vertebra and to collect different measurements to find the individual body size:
DarT Salmo-Eel (2022-2023)
Using samples across the entire range of species (Salmo salar, Anguilla anguilla and Salmo trutta), I am developing a library of neutral and potential locus SNPs under selections from DartSeq technology (2.5 million reads) to study the populations structure and history.
This project involves many partners (thirty institutions) in order to have the distribution of individuals over a minimum of 12 countries.
IRRAE (2021-2023)
Inventory of sharks and ray around Reunion island based on environmental DNA with an ecosystem approach (IRRAE).
In this project we optimized the sampling on boat and the molecular techniques of metabarcoding and barcoding with the design of 6 primers:
➢ Bulldog shark (Carcharhinus leucas)
➢ Tiger shark (Galeocerdo cuvier)
➢ Scalloped hammerhead shark (Sphyrna lewini)
➢ Tawny nurse shark (Nebrius ferrugineus)
➢ Giant guitar ray (Rhynchobatus djiddensis)
➢ Black-spotted stingray (Taeniura meyeni)
A total of 21 stations were carried out around Reunion over 3 seasons. We have just completed the samples in November 2022.
Funding by the DEAL and Region.
MAEO (2021-2023)
MAEO is the first Elasmobranch Observatory within the Mascarene Archipelago (MAEO) to enrich knowledge on the marine biodiversity of the western basin of the Indian Ocean..
This project is led by ARBRE in collaboration with the University of Mauritius and co-financed by the European Union within the framework of the PO INTERREG V OI and the Réunion Region.
MAEO provides rays and sharks data from scientific mission using underwater cameras and by the eco-participatory network.
Five main goals:
1. Characterize the elasmobranch populations present in the Mascarene Archipelago.
2. Study the spatio-temporal dynamics of the species.
3. Raise public awareness of the richness and conservation needs of marine ecosystems.
First picture competition of elasmobranchs in the southwest Indian Ocean:
POPSIZE (2020-2023)
The POPSIZE research project is part of the sustainable development objectives for fisheries to answer to the issues and challenges of stocks assessment, through two distinct but complementary objectives.
1) We propose to carry out an expanded inventory of the different methods to estimate the abundance of population (actual abundance and effective size) based on genetics tools, to test some of these methods on real and simulated datasets, and to provide recommendations in regard to their application in stock assessment of large pelagic fish. We have two real datasets, relating to two species monitored by RFMOs: albacore tuna (Thunnus alalunga) and blue shark (Prionace glauca). This project takes advantage of the latest technological and mathematical advances in order to i) test their effectiveness on target species and fisheries bycatch, and ii) assess the interest of a protocol including population genetics to support data on demographic trends acquired via traditional stock assessment methods.
2) This project also contribute to the dialogue between scientists and fishing professionals on the island of Reunion, through popularization tools and several direct meetings. Scientific results (ex. marine ecosystems of the Indian Ocean) are popularized and main themes most likely to interest fishing professionals are identified. We have hence set up two workshops bringing fishing professionals and scientists, and covering various themes. In addition, a study resulting from a questionnaire intended for professionals in the French large pelagic fishery was carried out during a tutored student project, in collaboration with the University of Pau, in order to better understand the expectations of professionals vis-à-vis scientists, their accessibility to the results and outcomes of stock assessments, as well as their needs and views on their own profession – see the report HERE: Analyse d’un questionnaire à destination des pêcheurs pélagiques professionnels français (ird.fr)
Bonus:
« The sea in all its states » is a project of documentary capsules, co-directed by the POPSIZE project and a regional funding fund released in support of the deployment of the Blue Institute with the aim of highlighting the different professions related to the marine environment. Two documentary capsules of 5 minutes each were shot as part of the project, in collaboration with Cerise sur le Gateau Prod:
• The first paints the portrait of an artisan mini-longline fisherman (small longline fishery), Kevin PAYET, also present at the two days of exchanges organized face-to-face on November 24, 2020 and May 10, 2021:
• The second retraces the events of the meeting workshop of November 24, 2020. It reports the proceedings and highlights of this day, but also the points of disappointment and areas for improvement suggested by the fishing professionals present:
Funding by:
Main Past projects
PALEOFISH (2021-2022)
In this project, the potential of archeological fish bones in recovering DNA of European Anguillidae and
Salmonidae has been anaysed.
A total of 163 fish bones supposed Anguillidae (65) and Salmonidae (98), mainly vertebrae, from paleolithic to the late medieval period were converted into Illumina next-generation sequencing libraries following a dedicated ancient DNA extraction protocol from about 30 mg of bone material on average. We then developed a workflow in Genotoul’s Galaxy to automate the data pre-processing (sequence clean-up and qualification pre/post clean-up), and alignment with reference genomes (FastQC, Fastp, BWA). We mapped all our individual sequence libraries against available Salmonidae and Anguillidae whole genomes from NCBI database, as well as other reference sequences for species of fish, bacteria, and vertebrates. Paleomix analysis have been done and detrmination of results in progress. The first results from Galaxy analysis revealed that most samples provided several millions of curated sequences reads and a high success rates of endogenous DNA. Genetic identification to the species level in Anguillidae and Salmonidae was also high. These estimates were a key to identify the potential in the use of calcified archaeological pieces in fish and will be the subject of a scientifc paper.
See the summary of the RIF conference: Bilan
sur l’accessibilité des ADNs à partir des pièces osseuses archéologiques chez
les les Anguillidae et Salmonidae européens – Archive ouverte HAL
(archives-ouvertes.fr)
MESOMAY & MESORUN (2021-2022)
Mesophotic Coral Ecosystems have been little studied in the South West Indian Ocean. The MesoRun and MesoMay program aims to make a non-exhaustive faunal inventory on certain sites located in the mesophotic zone (between 50 and 150 m deep) on the slopes of the reefs in Reunion and Mayotte islands. This program leds by Biorecif (Thierry Mulocheau) and Vie Océane, in collaboration with ARBRE, and funding by LIFE4BEST.
In this program, I was in charge of Work Package 2. The objective of this WP is to determine mesophotic diversity, using molecular tools including eDNA, to compare them with data provided by divers (photos, videos, and samples). Data on the microphytobenthos will also be necessary by taking small pieces of substrate, which will make it possible to acquire rare data concerning certain micro-algae in a mesophotic environment.
Here the report: Inventaire faunistique et floristique en zone mésophotique à La Réunion (archives-ouvertes.fr)
Two scientific papers are in preparation.
EFIMA (2017-2018 and -2020)
The first goal of this study was to optimize water filtration protocols on a small boat at sea and no cold chain storage to capture eDNA and to detect marine mammals. The second goal was to compare the marine mammals detections obtained via eDNA metabarcoding to visual monitoring (opportunistic sightings).
Samples were mainly collected in close proximity to marine mammals. Marine mammals off Reunion Island coasts were a good model since surveys have been conducted for many years and their aerial breathing can allow comparison between visual observations to molecular detections.
Two sets of primers were designed to target the hypervariable regions of mitochondrial 12S rRNA genes for vertebrates and mammals, respectively. DNA of Delphinidae was ubiquitous and successfully amplified with positive detections found in seven of the nine sightings. However, humpback whales were not successfully detected with the primers used, only two eDNA detections on the five sightings. Our study discussed of tasks for improvement and the power of using eDNA to monitor marine mammals in view of our knowledges to these species survey since 2008 in Reunion Island.
In 2021 and 2022, we added modelisation of surface particule to better understand the origin of eDNA function of oceanic currents.
Publication soon avalaible!
Report here: Rapport_EFIMA_ARBRE_V2.pdf (arb-reunion.fr)
Poster here: Programme EFIMA (2017-2018) – Agence de Recherche pour la Biodiversité à la Réunion (arb-reunion.fr)
Inventory of Fish Diversity using Genetic Tool (2017-2018)
Funding by RNNESP, it was the first project on eDNA in the souwest of Indian Ocean.
The aim of this study was to test whether the ichthyological diversity of one natural reserve in Reunion Island (Réserve de l’Etang de Saint-Paul) could be established with a molecular tool, environmental DNA (eDNA). We hence filtrated the water (2L) at 10 different areas around the reserve. For each sampling area, 12 PCR replicas were performed and the identification of fish species was carried out by metabarcoding through a primer over a mitochondrial region (12S). This study showed the importance of reference sequencing databases as well as improvements through phylogenetic analyses. This first fish study by eDNA in La Réunion also revealed the coherence of the distribution of species and their habitat.
GERMON (2012-2015)
The GERMON project had several aims i) to understand the populations’ structure between albacore tuna southwest of the Indian Ocean and southeast Atlantic, ii) to determine the origin of juveniles observed in South Africa iii) to improve the understanding of the biology field (Size and Weight relationship; reproduction and feeding area; trophic linkages) and iv) to initiate work on chemical analyzes and adaptation of the albacore species to its environment. These aims have been held and the results allow a better understanding of the management albacore.
Funding by the FEP (European Union).
Publications (9) in communications section.
Two movies on otoliths removal of swordfish and albacore in my section « Communication ». Swordfish otoliths are only a few millimeters long and few of us know how to extract them because of the tiny size and the large amount of white matter in and around the cranial box.
Report here: Projet GERMON. Structure génétique et migration du thon Germon (ifremer.fr)