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My PhD project aims to study fish biodiversity patterns across various habitats, using environmental DNA approaches. I study the diversity patterns on coral reefs across the world, and the biodiversity of fish on top of seamounts around the New-Caledonian archipelago, in order to assess the effects of environnemental, geomorphological and anthropogenic factors on fish distribution pattern.
High-throughput DNA sequencing is becoming an increasingly important tool to monitor and better understand biodiversity responses to environmental changes in a standardized and reproducible way. Environmental DNA (eDNA) from organisms can be captured in ecosystem samples and sequenced using metabarcoding, but processing large volumes of eDNA data a...
Increasing speed and magnitude of global change threaten the world’s biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct wel...
The intensification of anthropogenic pressures have increased consequences on biodiversity and ultimately on the functioning of ecosystems. To monitor and better understand biodiversity responses to environmental changes using standardized and reproducible methods, novel high-throughput DNA sequencing is becoming a major tool. Indeed, organisms she...
• Bioinformatic analysis of eDNA metabarcoding data is crucial toward rigorously assessing biodiversity. Many programs are now available for each step of the required analyses, but their relative abilities at providing fast and accurate species lists have seldom been evaluated. • We used simulated mock communities and real fish eDNA metabarcoding d...
Abstract for DNAQUA International Conference : international Conference on the Use of DNA for Water Biomonitoring - 2021
Project SEAMOUNTS aims to study the 3-dimensional distribution of vertebrate species diversity and abundance across 12 seamounts of the New-Caledonian archipelago to (i) better understand the influence of the human, environmental, geomorphological and ecological drivers, (ii) test hypotheses about the role of seamounts as oases of biodiversity, refuges for endangered species and stepping stone habitats, and (iii) inform decision makers about their conservation priority, if any. The project will combine two methods : eDNA and baited cameras (BRUVS).
eDNA is a fast-evolving tool to survey marine biodiversity, but the results depend greatly on the bioinformatic treatment done on the raw sequencing data. This project aims to compare the efficiency and accuracy of several specialized bioinformatic programs for each step of eDNA data analysis, and to produce the most performant pipeline.