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T H E S E Docteur En Sciences UNIVERSITE NICE-SOPHIA ANTIPOLIS - UFR Sciences Ecole Doctorale de Sciences Fondamentales et Appliqués T H E S E pour obtenir le titre de Docteur en Sciences de l'UNIVERSITE Nice-Sophia Antipolis Discipline : Sciences de l'Environnement présentée et soutenue par Giulia Prato Stratégie d'échantillonnage et modélisation trophique : des outils de gestion pour évaluer le fonctionnement des écosystèmes et le statut des prédateurs de haut niveau trophique dans les aires marines protégées méditerranéennes. Field monitoring and trophic modelling as management tools to assess ecosystem functioning and the status of high trophic level predators in Mediterranean Marine Protected Areas Thèse dirigée par et codirigée par Patrice FRANCOUR Didier GASCUEL soutenue le 29 janvier 2016 Mme. Marta COLL Docteur Rapporteur M. Giuseppe DI CARLO Docteur Examinateur M. Patrice FRANCOUR Professeur Directeur de thèse M. José GARCIA CHARTON Professeur Rapporteur M. Didier GASCUEL Professeur Directeur de thèse M. Paolo GUIDETTI Professeur Président du jury Abstract The overexploitation of high trophic level predators (HTLP) may trigger trophic cascades, often leading to a simplification of marine food-webs and reducing their resilience to human impacts. Marine protected areas (MPAs) can foster increases of HTLP abundance and biomass, but long time frames are needed to observe a recovery, when possible, of lost trophic interactions. This PhD aimed to propose integrated management-tools to monitor HTLP recovery and the restoration of trophic interactions in Mediterranean MPAs, and to evaluate the effectiveness of these tools at assessing fishing impacts upon HTLP and the associated food-web. Two often distant approaches were combined: field monitoring and food-web modelling. First, to survey the fish assemblage, we proposed to improve the traditional underwater visual census technique of one size-transects with variable size transects adapted to fish mobility. This improvement increased the accuracy of density and biomass estimates of HTLP at three Mediterranean MPAs. We then evaluated the potential of food-web modelling with the Ecopath with Ecosim and Ecotroph approach as a tool to inform ecosystem-based management in Mediterranean MPAs. We proposed a standard model structure as the best compromise between model complexity, feasibility of model construction in terms of data collection, and reliability of model outputs. Key functional groups for which local accurate biomass data should be collected in priority in order to get reliable model outputs were identified. Applying this approach to an old data- rich MPA allowed to highlight the keystone functional role of HTLPs and cephalopods, and to assess the cumulated impact of artisanal and recreational fishing on the food-web. Model outputs highlighted that reducing recreational fishing effort would benefit both the ecosystem and the naturally declining artisanal fishery, through increased availability of higher quality catches. Finally, we estimated the costs of model development for a data- poor reserve and suggested how to cost-efficiently increase model quality. Overall this PhD work emphasised the potential of combining field monitoring and food- web modelling tools, which can mutually enhance each other to achieve an effective ecosystem based management in MPAs. Abstract FranÇais La surexploitation des prédateurs de haut niveau trophique (HTLP) peut déclencher des cascades trophiques qui souvent conduisent à une simplification des réseaux trophiques marins en réduisant leur résistance aux impacts humains. Les aires marines protégées (AMP) peuvent favoriser des augmentations d’abondance et biomasse des HTLP, mais la complète restauration des interactions trophiques, lorsque cela est possible, nécessite des délais importants. Cette thèse vise à proposer des outils intégrés de gestion pour évaluer le retour des HTLP et la restauration des interactions trophiques dans les AMP méditerranéennes, et à évaluer l’efficacité de ces outils pour estimer les impacts de la pêche sur les HTLP et le réseau trophique associé. Deux approches souvent éloignés ont été combinées : les suivis de terrain et la modélisation des réseaux trophiques. Pour échantillonner la communauté de poissons, nous avons proposé d'améliorer la technique traditionnelle de recensement visuel sous-marin en recourant à des transects de taille variable, adaptée à la mobilité des poissons. Cette méthode a lors permis d'augmenter la précision des estimations de densité et de biomasse des HTLP dans les trois AMP méditerranéennes suivies. Ensuite, nous avons évalué l'apport de la modélisation trophique avec les approches EwE et EcoTroph comme outil de gestion écosystémique pour les AMP méditerranéennes. Une structure standard de modèle a été proposée comme étant le meilleur compromis entre la complexité du modèle, la faisabilité de sa construction et la fiabilité de ses sorties. Les groupes fonctionnels clés pour lesquels des données de biomasse locales exactes devraient être recueillis en priorité afin d'obtenir des sorties de modèles fiables ont été identifiés. L'application de cette approche à une AMP ancienne, riche en données, a permis de mettre en évidence le rôle fonctionnel clé des HTLP et des céphalopodes, et d'évaluer l'impact cumulé de la pêche artisanale et de loisir sur l'ensemble du réseau trophique. Les résultats du modèle ont montré qu’une réduction de l'effort de la pêche de loisir profitait à la fois l'écosystème et améliorait la rentabilité de la pêche artisanale, grâce à une disponibilité accrue des captures de niveau trophique supérieur. Enfin, les coûts de développement d'un tel modèle pour une AMP ne disposant que de peu de données ont été estimés, tout en suggérant des pistes pour améliorer la qualité du modèle. Globalement, ce travail de thèse a souligné le potentiel d'une approche conjuguant des suivis de terrain et de la modélisation trophique, des outils se renforçant mutuellement, pour parvenir à une gestion écosystémique efficace dans les AMP. TABLE OF CONTENTS 1. Chapter 1. General introduction ...................................................................................... 1 1.1 The ecological importance of high trophic level predators. .................................. 1 1.2 High trophic level predators recovery in Mediterranean Marine Protected Areas and related management challenges ............................................................................. 3 1.3 Thesis objectives and approaches ....................................................................... 4 1.4 Structure of the manuscript .................................................................................. 6 2 Chapter 2. The importance of high-level predators in marine protected area management: Consequences of their decline and their potential recovery in the Mediterranean context. Prato G, Guidetti P, Bartolini F, Mangialajo L, Francour P (2013). Advances in oceanography and Limnology 4:176–193 ....................................... 15 Section 1. Field monitoring .................................................................................................... 34 3 Chapter 3. Reviewing fish underwater visual census methods in the Mediterranean Sea: setting a baseline for standardisation. .......................................... 35 3.1 Abstract .............................................................................................................. 35 3.2 Introduction ......................................................................................................... 36 3.3 Methods .............................................................................................................. 38 3.3.1 Bibliographic review ..................................................................................... 38 3.3.2 Field methods comparison ........................................................................... 39 3.3.3 Integration of bibliographic and field work .................................................... 40 3.4 Results ............................................................................................................... 42 3.4.1 Bibliographic review ..................................................................................... 42 3.4.2 Field methods comparison ........................................................................... 48 3.4.3 Integration of bibliographic and field work .................................................... 51 3.4.4 Transects standardisation across the Mediterranean .................................. 55 3.5 Discussion .......................................................................................................... 55 3.6 References ......................................................................................................... 60 3.7 Annex ................................................................................................................. 66 4 Chapter 4. Combining multiple underwater visual census transect sizes to survey the whole fish assemblage in Mediterranean marine protected areas: an application in 3 case studies ................................................................................................. 82 4.1 Abstract .............................................................................................................. 82 4.2 Introduction ......................................................................................................... 84 4.3 Methods .............................................................................................................
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