Thèse Renforcer la Résilience des Dunes Face aux Impacts Anthropiques aux Espèces Végétales Exotiques Envahissantes et au Changement Climatique H/F - 66

Établissement : Université de Perpignan Via Domitia
École doctorale : Energie et Environnement
Laboratoire de recherche : Laboratoire Génome et Développement des Plantes
Direction de la thèse : Moaine EL BAIDOURI ORCID 0000000250233457
Début de la thèse : 2026-07-01
Date limite de candidature : 2026-04-07T23:59:59

Les systèmes dunaires côtiers sont des écosystèmes dynamiques et multifonctionnels qui jouent un rôle clé dans la protection du littoral, la conservation de la biodiversité et la valeur paysagère, en particulier dans le contexte méditerranéen. Cependant, ils sont de plus en plus menacés par les effets combinés du changement climatique, des espèces végétales exotiques envahissantes, de l'altération des dynamiques sédimentaires et des pressions anthropiques (urbanisation, tourisme et infrastructures côtières). Ces facteurs perturbent la composition des communautés végétales, le fonctionnement géomorphologique et la connectivité des populations, affaiblissant la résilience des dunes et compromettant leur rôle de solutions fondées sur la nature pour la lutte contre l'érosion et les submersions marines. Malgré les efforts croissants de restauration, d'importantes lacunes subsistent sur (i) l'adéquation écologique et la localisation des plantations, (ii) la provenance génétique des semences/plants utilisés, et (iii) l'ampleur réelle et les facteurs des invasions biologiques en milieux sableux côtiers.

Ce doctorat s'inscrit dans l'AFLE (Aire Fonctionnelle Littorale Est), région transfrontalière franco-espagnole du nord-ouest de la Méditerranée qui englobe une grande diversité de milieux géomorphologiques, de régimes de gestion et statuts de conservation des espèces, et où les dunes naturelles ne représentent plus que 16 % du linéaire côtier. Cette région constitue un laboratoire à ciel ouvert idéal pour des analyses comparatives des systèmes plage-dune, allant de contextes fortement urbanisés à semi-naturels ou protégés. Ce territoire est soumis à une forte pression humaine, à des modifications anciennes du trait de côte et à une gouvernance fragmentée, tout en abritant des habitats dunaires d'intérêt patrimonial et des espèces végétales menacées ou endémiques.

L'objectif de ce projet est d'améliorer la résilience et la stabilité fonctionnelle des dunes méditerranéennes en reliant la dynamique des communautés végétales, la pression exercée par les espèces exotiques envahissantes et les processus génétiques à l'échelle des populations afin d'orienter les actions de conservation et de restauration fondées sur des données scientifiques. Trois objectifs structurent les activités de recherche : (i) évaluer la composition des communautés végétales, la richesse spécifique et la structure de la végétation dans des systèmes plages-dunes contrastés afin de quantifier l'intégrité et l'état de succession écologique ; (ii) évaluer la répartition, les facteurs déterminants et les impacts des espèces exotiques envahissantes afin d'éclairer les mesures de gestion adaptées au contexte et tenant compte de la géomorphologie ; (iii) évaluer la diversité génétique et la structure des populations pour orienter les stratégies de renforcement des populations et de flux génétique assisté qui favorisent leur persistance à long terme. Une attention particulière sera accordée aux espèces spécialisées et menacées des dunes tels que Achillea maritima, afin d'évaluer les goulets d'étranglement démographiques, l'érosion génétique et l'efficacité des efforts de translocation passés.

Les résultats attendus incluent l'identification de décalages entre pratiques de restauration et fonctionnement naturel (espèces implantées hors niche écologique/géomorphologique ou issues de pools génétiques non locaux), ainsi qu'une évaluation intégrée de la répartition des invasions biologiques dans les dunes de l'AFLE, en lien avec l'usage des sols, la gestion et la géomorphologie. En combinant approches communautaires, paysagères et génétiques des espèces, le projet produira des recommandations opérationnelles pour une restauration et une conservation des dunes cohérentes écologiquement, informées génétiquement et transférables à d'autres régions côtières méditerranéennes et européennes.

Coastal dunes constitute a primary line of defence against storm-induced erosion and flooding, functioning as nature-based infrastructures that protect inland areas (White et al., 2024). Their development and stability are tightly controlled by vegetation, particularly pioneer communities in the foredune, whose root systems are adapted to wind exposure, sand burial, and storm disturbance, enabling efficient aeolian sand trapping and dune growth (Durán & Moore, 2013; Bazzichetto et al., 2020). Vegetation diversity enhances surface cover and belowground biomass, thereby increasing resistance to wave impact and improving post-storm recovery (White et al., 2024). These systems are organised along a marked sea-inland zonation that hosts highly specialised and often endemic plant communities, making coastal dunes biodiversity hotspots despite their relatively low species richness (Angiolini et al., 2018; Pintó et al., 2023).
Despite their ecological and geomorphological importance, coastal dunes are among the most threatened ecosystems in Europe, with around 70% lost over the last century, particularly in the Mediterranean due to urbanisation, tourism, and mechanical beach management (Pintó et al., 2023). Disturbance alters vegetation spatial patterns, reduces ecological functionality, and disrupts successional dynamics, while soil properties and microtopography remain key determinants of species composition (Angiolini et al., 2018). Recent advances highlight the critical role of deep belowground biomass for dune resistance during extreme events and reveal that managed or artificially constructed dunes often show reduced resilience compared to natural systems (White et al., 2024). Consequently, restoration strategies are shifting towards successional facilitation approaches and the use of ecological integrity indicators to guide management (Pintó et al., 2023; Fischman et al., 2024).
Within this context, IAS pose a major threat by reducing habitat diversity and impairing dune capacity to adapt to sand mobility and increasing storm intensity, yet their direct links with geomorphology and management remain poorly quantified (Ciccarelli & Bacaro, 2016; Pintó et al., 2023). Climate change further complicates invasion dynamics, with recent projections showing that many invasive plants may lose climatic suitability while a smaller subset expands, leading to a redistribution rather than a uniform intensification of invasion pressure (Collette et al., 2026). At the same time, rare and threatened dune specialist species face increasing demographic and genetic bottlenecks as a consequence of habitat fragmentation, reduced population sizes, and disrupted connectivity. These processes erode genetic diversity, limit adaptive potential, and may ultimately lead to local or regional extinctions. In such contexts, habitat restoration alone is often insufficient, and complementary conservation interventions become necessary. Assisted gene flow and plant translocations-through the deliberate introduction of seeds or individuals into genetically depauperate, isolated, or extirpated populations-have therefore emerged as key tools alongside ecological management. However, recent assessments across Europe reveal low long-term success rates for plant conservation translocations, with fewer than one-third of populations becoming self-sustaining and with genetic monitoring rarely implemented (Godefroid et al., 2025). These limitations underscore the need to integrate genomic approaches into translocation planning and evaluation, in order to guide source population selection, assess genetic compatibility, and identify barriers to persistence. Dune specialists such as Achillea maritima, a critically endangered Mediterranean species with a history of repeated translocation efforts, provide a particularly relevant model for advancing genomics-informed conservation and restoration strategies in coastal dune systems. Together, these challenges highlight the need for integrated approaches that link vegetation composition, geomorphology, IAS dynamics, and population genomics to support effective, climate-adaptive conservation and restoration of coastal dune systems.

Objective 1: Assessing plant communities composition and richness

Using representative set of plots across natural, semi-natural, semi-urban, and urban beach-dune systems, the aim of this objective is to 1) assess plant community composition, cover, and species richness along the beach-dune zonation using Braun-Blanquet methods; 2) identify plant species most suitable for increasing dune volume by relating species distribution and cover to geomorphological characteristics; and 3) map current bioclimatically suitable areas for 36 dune-specialist plant species within the AFLE region, forecast their future extent and dynamics under multiple climate scenarios by the end of the 21st century, and identify potential climatic refugia for the period 2081-2100.

Objective 2: Assessing invasive alien species invasions to guide context-dependent management frameworks

Using a two-phase approach, the aim of this objective is to 1) identify and map all invasive alien plant species present along the AFLE coast and quantify the surface area they occupy within beach-dune systems, and 2) apply species distribution modelling, following an approach similar to that developed for the Pyrenees (Collette et al., 2026), to assess future climatic suitability and distinguish potential winner and loser species under climate change in order to support context-dependent management and control strategies.

Objective 3: Assessing genetic diversity of threatened natural populations to guide population reinforcement strategies

Using genomic approaches, the aim of this third objective is to 1) clarify the taxonomy of Achillea maritima by determining whether it comprises a single taxon or two sub-species, atlantica and maritima. While the atlantica subspecies is less threatened, the mediterranean maritima subspecies is critically endangered in France and already extinct from North Catalonia where it is only preserved in herbaria, 2) assess the genetic diversity of actual remaining natural populations implementing ten of thousands polymorphic markers thereby substantially improving upon previous work based on a single gene with limited variation, which identified only three Mediterranean haplotypes and failed to resolve subspecific differentiation (Doran, 2024), 3) take up the challenge of comparing comtemporary diversity with historical diversity inferred from herbaria, 4) assess the genetic admixture in targeted self-sustaining translocated sites established two decades ago compared to not persisting or not self-sustaining ones in order to unravel barriers to successful translocations.

Objective 1: Assessing plant communities composition and richness

The PhD student will assess plant community composition and richness across coastal dune systems within the AFLE region using a stratified sampling design that captures urban, semi-urban, and semi-natural beaches, as well as contrasting geomorphological settings and management regimes. This approach will allow evaluation of the relative influence of management practices and geomorphology on vegetation structure. Floristic surveys will be conducted by the candidate along shore-perpendicular transects following the natural beach-dune zonation and recorded in contiguous 2 m² plots, and species presence, abundance, and cover will be estimated using the Braun-Blanquet method. The student will characterise community structure, successional stage, and ecological integrity, to relate floristic richness and dune-specialist species to geomorphological features and management practices.

Objective 2: Invasive alien species assessment

The PhD student will assess IAS in coastal dune systems by combining bibliographic synthesis with field data. A list of IAS reported in AFLE dune environments will be compiled from the literature and existing databases and integrated with long-term datasets from the UdG research group. Targeted surveys will quantify IAS abundance, spatial distribution, and position along the dune zonation, and relate their occurrence to geomorphological characteristics and management variables, in order to support context-dependent prioritisation of IAS control. The PhD student will then apply ensemble species distribution models, building on recent work combining IAS occurrence data and bioclimatic variables, to evaluate current and future invasion risks. While previous projections focused on the Pyrenean range, this PhD will extend modelling to the AFLE region under multiple climate scenarios (2021-2100) to inform coastal conservation and management strategies.

Objective 3: Population genomics for natural or translocated individuals and herbarium specimens

Non-invasive sampling and the use of reduced representation genomic approaches (genotyping-by-sequencing protocol called nGBS, transcriptomics) will be performed by the PhD student to conduct population genomic studies. His/her challenge within this project will be to include herbarium samples to bridge the gap in our understanding of past and present genetic diversity. Ancient DNA from herbaria are frequently damaged and fragmented, therefore he/she will have to optimize DNA extraction and adapt short-read sequencing protocols either excluding the fragmentation step in library preparation or using target enrichment and genome skimming (Hyb-seq). The student will benefit from the expertise of the GENO'MIX team (LGDP/UPVD) in population genomics and developing bio-informatic pipelines to investigate the degree of diversity, inbreeding and connectivity between populations and provide a better understanding of their demographic history (Salvado et al., 2022; Salvado et al., 2026). These pipelines can be processed with or without a reference genome but the student will have to implement a combination of both ancient and recent data in his/her analysis.

Objective 1 and 2: Vegetation and IAS data analysis

The student will use multivariate statistical techniques, including ordination methods and mixed-effects models, to analyse vegetation and IAS data and explore relationships between community composition, environmental variables, geomorphology, and management practices. In addition, morphological data are available through the databases of the LAGP/UdG from previous and ongoing projects, including vegetation samples, high-resolution datasets derived from remote sensing. These datasets incorporate information acquired using sensors mounted on unmanned aerial vehicles (UAVs) and ground-based platforms such as terrestrial LiDAR, allowing detailed characterisation of dune morphology, microtopography, and structural attributes, which will be integrated into the analyses where relevant.