ZHYBRID-E - Thesis 2024-2027
BIOSEFAIR
Vertical headings
Our actions
PhD projects
ZHYBRID-E - Thesis 2024-2027

ZHYBRID-E Detection of hybrid zones in aquatic environments and response to climate change by e-barcoding

Anthropogenic pressure on aquatic environments in the SOUTH region is intensifying, amplified by marked climate warming. It manifests as habitat fragmentation, reduced river flow, and warming of water bodies, leading to impacts on fish growth, reproduction, tolerance to hypoxia, and resistance to parasites and contaminants. When these constraints become too severe, multiple hybridizations emerge, linked to the overlap of ecological niches. In this context, the assessment of hybridization rates appears essential, but its implementation on a large scale remains technically and financially challenging. The advent of metabarcoding and environmental barcoding (non-invasive, rapid, inexpensive) allows for a considerable reduction of sampling efforts and species-level identifications.

  • Starting date: 1st october2024
  • Research Unit: UMR RECOVER
  • INRAE Site: PACA
  • PhD Director: Martin Daufresne et Nicolas Pech
  • Additional Supervisor: André Gilles
  • PhD Student: Azélie Buisson
  • University and Doctoral School: Aix-Marseille Université, ED 251Sciences de l'environnement
  • Funding: Métaprogramme Biosefair / Région Sud / AMU
  • Disciplines involved: aquatic ecology, genomics, population genetics, modeling, bioinformatics, biodiversity management 

Objectives

The PhD project aims to develop a tool for detecting where pure and hybrid individuals coexist within fish populations, based on the use of environmental DNA.

The objectives are to:

  • Develop around thirty independent nuclear markers representative of the genome of the species studied and compare them with a mitochondrial marker;
  • Model the absence of hybridization by testing the congruence of the different nuclear markers (mitochondrial and nuclear), knowing that incongruence reflects a hybridization process;
  • Validate the effectiveness of the tool in mesocosms and in natura.

Approaches

The first step will consist of selecting in silico around thirty orthologous gene sequences of about 100 bp from a database containing more than 25,000 genes. We will target the most variable genes in the species of interest, mainly Parachondrostoma toxostoma (Toxostome), Telestes souffia (Blageon), and Chondrostoma nasus (Hotu). Amplification protocols will be optimized and tested on mesocosms containing pure individuals, F1 and F2 hybrids in order to calibrate hybrid detection, before applying them to eDNA from study sites known to host hybrid individuals.

The development of the protocol and modeling will be reinforced by data from our mesocosms (pure and hybrid individuals), before being perfected and applied in the field.

Fieldwork (fishing campaign and eDNA ) will focus on several stations:

  • the Rhône basin hosting populations of Toxostoma, Blageon, and Hotus, in parapatry or sympatry, with or without signs of hybridization;
  • the Argens basin (in collaboration with the « Syndicat Mixte de l'Argens »), where populations of Barbus barbus and Barbus meridionalis coexist, with the aim of methodological transfer for routine use of the developed tool.

Contacts

Modification date: 26 November 2025 | Publication date: 26 November 2025 | By: Azélie Buisson