Supervision
Post-Doctorate
L2020-2022 (IRD – MARBEC)
Work on both goals of POPSIZE project: i) improvement and evaluation of methods for estimating population abundance and ii) to promote a dialogue between scientists and fisheries professionals.
Post-Doctorate: Chrystelle Delord
Supervision: Natacha Nikolic, Francis Marsac (IRD), Sophie Arnaud-Haond (Ifremer)
PhD
January 2024-December 2026
From landscape ecology to territorial planning: towards integrated management of the coral reefs of La Réunion.
Doctorant: Léo Broudic
Supervision: Benjamin Bergerot (ECOBIO) & Camille Mazé (CEVIPOF), co-supervision Mathieu Pinault (MAREX), Natacha Nikolic (ARBRE, INRAE, CRBE), et Touria Bajjouk (Ifremer).
December 2022-December 2025 (INRAE, AQUA):
Evolutionary history of two migratory species, the European eel and the Atlantic salmon: inferences from demographic and selective history from ancient and modern DNAs.
Doctorant: Patrick Jacques (Education Master Computational Biology – University Bordeaux)
Supervision: Natacha Nikolic
Master
January to June 2024
Projet DeFIS (Detection of Fauna and flora: Identification of Species)
Report here: (PDF) Projet DeFIS (Detection of Fauna and flora: Identification of Species) (researchgate.net)
Emergence of the DeFIS pipeline, which allows the comparison of samples to a reference genome database to determine their species using the k-mer method, with assessments of index and representativeness, facilitating comprehensive results. The pipeline is primarily intended for researchers working on ancient or environmental DNA samples. The application of the pipeline to European diadromous fish data enabled the development of a reference genome repository and a k-mer library for the genetic identification of diadromous species.
January to June 2024
Enhancement of Knowledge on the Platyhelminthes of Reunion Island: Species Identification, Distribution, and Preferential Environmental Factors
co-Trainee: Raphaëlle Pasco (Master II – Univerity La Réunion)
Report here:
March-July 2023 (INRAE)
Ichthyological taxonomic inference from environmental DNA data: example of mesophotic and tropical ecosystems
Trainee: Anaïs Paullin-Fayolle (Master I UPPA – France)
January-July 2022 (ARBRE)
Biodiversity and spatial distribution of elasmobranchs in the Mascarene Archipelago.
Trainee: Laure Inçaby (Master II UPPA – France)
July-October 2022 (ARBRE, Inexence, MAREX)
Literature review – Artificial reefs based on gabions.
Literature review and a concept study to achieve these purposes:
– To break the swell by associating both free riprap associated with a peripheral defense of gabion and flexible gabion mattresses fixed to the ground and linked together.
– Reinforce the coral reef by promoting the proliferation of corals through ecological engineering.
Trainee: Marius Molinet (Environmental Engineer, Institut Agro Montpellier – France)
Report here:
March to July 2022 (ARBRE, Cetasea, Duocéan and partners)
Behavioral study of bottlenose dolphins (Stenella longirostris) and Indian Ocean bottlenose dolphins (Tursiops aduncus), in the presence of divers in a of divers in passive observation situation.
This study was part of a framework of understanding passive tourist activities of cetacean observation, for a better for a better conservation management of dolphins in Reunion Island.
Trainee: Camille Bourhis (Master Ethology-Ecology – Jean Monnet University – SAINT ETIENNE)
Report here: (PDF) Stenella longirostris and Tursiops aduncus behavior’s study in presence of passive divers (researchgate.net)
January to July 2022 (INRAE)
Genetic analysis in the European eel (Anguilla anguilla).
Using a large genetic dataset from 174 European eel (Anguilla anguilla) individuals from 12 different countries over time periods ranging from the High Roman Empire to the present time, a SNP (Single Nucleotide Polymorphism) library was constructed under Diversity Arrays Technology (DArT). The construction of this library has been realized with the help of computer filtration and population genetics analyses. Beyond presenting this library of 16,150 SNPs, this work presents the preliminary results on the diversity and population structure analysis. However, we will see that additional samples are necessary to confirm or refute these results on genetic differentiation. The results are consistent with the geographic origin of the individuals with a significant genetic distance between them. Finally, the detection of potential neutral and under-selected SNPs, included in this library, allowed us to identify 776 potentially under-selected SNPs with a wide range of biological functions (e.g. calcium signaling, ABC transporter and circadian rhythm) that could be used for further studies.
Trainee: Olivier Larousse (INSA, Toulouse)
September 2021-February 2022 (INRAE, IRD)
Tutored project Master II UPPA
Inference about genetic demographic and population management of albacore.
The purpose of this project was to use microsatellite genotyping data on albacore tuna (2316 individuals and 32 neutral markers) to differentiate populations and evaluate their genetic diversity.
Trainee: Cassandra Clément, Helias Guiraud, Laure Inçaby, Lisa Loze, and Léa Simonet
September 2020-February 2021 (INRAE, IRD)
Tutored project Master II UPPA
Analysis of a questionnaire for French professional pelagic fishermen.
Within the framework of a POPSIZE project, a questionnaire aimed at French pelagic fishers was set up to better understand their expectations towards scientists, their visions on stock assessments, as well as their needs and views on their own profession.
This questionnaire was constructed to address several dimensions:
– Category of fishery (questions from 1 to 6).
– Personal state (human dimension) (questions 7 to 10).
– Link with scientists (dimension of the fisher-scientist link) (questions from 11 to 20).
– Expectations of external actors (questions from 21 to 25).
The purpose of this tutored project was initially to continue the transmission of this questionnaire to all the fisheries committees at the national level in order to collect more data. To date, about sixty fishermen have responded. In a second step, these data were analyzed to evaluate all the study dimensions. Finally, the results were discussed in order to improve the points raised (e.g. how to strengthen the link between scientists and fishermen; which tools could improve the accessibility of fisheries knowledge and a better visibility (and understanding) of the stock assessments for the fishermen; etc.).
Trainee: Coline Arqué, Charlotte Couëdel, Sven Mellaza, Marylou Pourret, Axel Rochaud
Report here: Analyse d’un questionnaire à destination des pêcheurs pélagiques professionnels français (ird.fr)
2018-2019 (University la Réunion, MNHN, ARBRE)
Tutored Master II project on only the genetic part with Agnès Dettaï (MNHN)
Metabarcoding on marine species from ARMs (Autonomous Reef Monitoring Structures) in the souwest Indian Ocean.
Trainee: Emmanuelle Waguette (University Bretagne Occidentale)
2014-2015 (Ifremer)
Analyses of fisheries data (historical series) on albacore tuna Thunnus alalunga, in the Northeast Atlantic.
Fishing catches and vessel characteristics have long been used to assess the abundance of stocks of marine resources. In order to access indices of abundance of exploited species, CPUEs can be used, as is the case for pelagic species such as tuna. The relationship between CPUEs and abundance can be very weak. Indeed, CPUEs can also reflect changes in catchability (Clark, 1985) which depends on the behavior of the fish in the water column, weather conditions, the gear used, and the fishermen. The work carried out during this training period has provided data on albacore tuna exploited by the French fisheries in the North Atlantic as well as a better understanding of these data through classical statistical approaches. This internship also touched on the aspect of change in environmental parameters and abundance using scripts for the extraction of environmental data (e.g. surface temperatures) and the use of linear and additive models. Troll and live bait (with rods) catch data from 1967 to 1986, on the French fleets and albacore in the Northeast Atlantic, were used to estimate indices of stock abundance, via CPUEs in previous studies (Goujon, 1996). The models have allowed the standardization of CPUEs in order to assess albacore stocks and provide a diagnosis for fishery managers. Concerning our data on French pelagic trawlers from 1991 to 2014.
Trainee: Audrey Patucca (Master II UPPA)
License
March-May 2022 (INRAE)
Genetic analysis and phylogeny on European eel (Anguilla anguilla).
Preliminary analysis on Dart-Sequencing data on European eel to built a library, and to learn basis on genetic diversity and phylogeny analysis.
Trainee: Camille Pery (License 3 UPPA)
Summer 2022
Phylogenetic analysis of ichthyological sequences of environmental DNA.
Mayotte is one of the places with one of the richest marine biodiversity of the territory. In order to preserve it and to evolve without altering it, a non-invasive molecular tool has been used to carry out biodiversity inventories by detecting the species present in the habitats. This tool is called environmental DNA (eDNA).
In the framework of this internship, Florian participated in the genetic analysis of eDNA sequences and more particularly those of the fish fauna from the MesoMay program. The objective of this program was to make a non-exhaustive faunal inventory in the mesophotic zone on the reef slopes of Mayotte.
Trainee: Florian Campagnari (INP, Purpan)
Report here: http://dx.doi.org/10.13140/RG.2.2.16667.75044
April-June 2021
Bio-empathy and positive biodiversity
Implementation of a bibliographic and psychological work (via the production and analysis of a questionnaire) to shed light on the concept of « emotional biodiversity » by measuring it in school children, 8 to 12 years old, in Reunion Island. More specifically, this work has taken stock of the factors and processes that lead children to act in favor of the preservation of nature and biodiversity. This project was carried out in collaboration with teacher-researchers specialized in Environmental Psychology (Univ. De la Réunion), Amandine Junot and Yvan Paquet, and researcher in Biology (Thomas De Solan).
Trainee: Coline Hervoche (Licence 3, UBS)