Models of General Community Assembly Mechanisms Simulating the Spatial and Temporal Dynamics of Benthic Biodiversity Nikolaos Alexandridis

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Models of General Community Assembly Mechanisms Simulating the Spatial and Temporal Dynamics of Benthic Biodiversity Nikolaos Alexandridis Models of general community assembly mechanisms simulating the spatial and temporal dynamics of benthic biodiversity Nikolaos Alexandridis To cite this version: Nikolaos Alexandridis. Models of general community assembly mechanisms simulating the spatial and temporal dynamics of benthic biodiversity. Earth Sciences. Université de Bretagne occidentale - Brest, 2017. English. NNT : 2017BRES0031. tel-01590621 HAL Id: tel-01590621 https://tel.archives-ouvertes.fr/tel-01590621 Submitted on 19 Sep 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE / UNIVERSITÉ DE BRETAGNE OCCIDENTALE présentée par sous le sceau de l’Université Bretagne Loire Nikolaos Alexandridis pour obtenir le titre de DOCTEUR DE L’UNIVERSITÉ DE BRETAGNE OCCIDENTALE Préparée à IFREMER/DYNECO/LEBCO Mention : Biologie Marine et UBO/IUEM/LEMAR École Doctorale des Sciences de la Mer Thèse soutenue le 28 mars 2017 Models of general devant le jury composé de : community assembly Marta COLL MONTON PhD, ICM-CSIC / rapporteur mechanisms simulating Peter HERMAN PhD, Professeur, Deltares / rapporteur the spatial and temporal Anik BRIND'AMOUR dynamics of benthic PhD, IFREMER / examinatrice biodiversity Jeffrey M. DAMBACHER PhD, CSIRO / examinateur Cédric BACHER PhD, HDR, IFREMER / directeur de thèse Frédéric JEAN PhD, Professeur, UBO / directeur de thèse Le travail de préparation de cette thèse de doctorat a été financé par Ifremer et la Région Bretagne. Le projet français LabexMer (ANR-10-LABX-19-01) a soutenu financièrement les travaux. The work for the preparation of this PhD thesis was funded by Ifremer and the Region of Brittany. Financial support was provided by LabexMer French project (ANR-10-LABX-19-01). Acknowledgements The completion of this thesis would not have been possible without the generous help of people who happily exceeded their obligations. Those individuals deserve much of any credit that may be given for this thesis and none of the criticism. First, I would like to thank my supervisor, Cédric Bacher, whose unwavering belief in the topic he conceived himself and trust in me made this thesis possible. A true chercheur sans peur et sans reproche, through his courageous support and insightful direction, he has worked tirelessly to improve the thesis and myself. He has nobly set a standard against which I will have to measure my future efforts. Second, I want to thank my supervisor, Fred Jean, for being available every time I needed his help. When I felt overwhelmed by the complexity of the natural and scientific world, the clarity and the scope of his vision would effortlessly put things into perspective. He has been le bon chercheur, an example of how the essence of good science lies in cognitive flexibility and profound humanity. Many parts of this thesis owe their existence to the inspiring work of Jeffrey M. Dambacher. Both as a teacher and as a collaborator, he has been so generous with his personal drive and expertise, that I could not help realizing the degree of my privilege and the social responsibility that ensues. The work of this thesis would have been a mere theoretical exercise of a much narrower outlook without the connection to the natural world granted by the willingness of Nicolas Desroy to share his hard-earned data set and his thorough understanding of the functioning of the Rance estuary. Many people from various parts of the world offered valuable advice during the preparation of this thesis and attempting a full account here would be an exercise in futility. There are, however, three individuals whose contribution stands out in both qualitative and quantitative terms. Claire Chevalier, Stanislas F. Dubois and Antoine Carlier have always been extremely responsive and effective at transferring their unparalleled knowledge of marine benthic biology, more often than not resisting the temptation to poke fun at my ignorance or the simplifying imperative of modelling. I would also like to express my deepest gratitude to the members of the thesis defence jury, Anik Brind'Amour, Marta Coll Monton and Peter Herman, as well as the members of the thesis committee, Nathalie Niquil and François Le Loc'h. Their contribution far exceeded my expectations and is akin to a gift that keeps on giving, as I grapple with the yield of their immense combined intellect. Speaking of immense combined intellect, special thanks go to my dear office mates, Auriane Jones, Thibault Androuin, Alexandre Robert and Térence Desclaux. I am honoured by their friendship and proud to have called them my colleagues. Their enthusiasm and integrity gives me confidence in the future and longing to see our paths cross again soon. I am also grateful to Philippe Cugier, Olivier Gauthier, Patrick Le Mao, Richard Little, Elizabeth Fulton, Sebastien Rochette, Thomas Yoann, Martin Marzloff, Flavia Nunes, Amelia Curd, Aline Blanchet, Touria Bajjouk, Celine Cordier, Clémence Caulle, Alain Menesguen, Jacques Populus, Xavier Caisey, Carlos Guallar, Fernando Tempera, Jill Sutton, Mathilde Cadier, Aridane González, Ilian Decorte, Elisabeth Bondu and Jacqueline Quentel for their ample assistance and inspiration. Finally, many thanks to Thomas Gregoris, Aloïs Hachet, Vincent Vallée, Lise Bacouillard, Laure Régnier, Angelica Navarro and all the interns and staff of i IFREMER/DYNECO/LEBCO and UBO/IUEM/LEMAR who created the at once welcoming and challenging working environment that every scientist should enjoy. I plan on thanking my friends and family in person. Should, contrary to expectations, any of them make it this far into my thesis and miss their name, next round is on me. ii Résumé détaillé Les macroinvertébrés benthiques entretiennent un ensemble complexe d’interactions avec leur environnement abiotique, leurs ressources et entre eux. Les échelles spatiales et temporelles des processus formant la base de ces interactions ont traditionnellement limité leur étude empirique et le développement de modèles statistiques. Les modèles mécanistes, n’ayant aucune contrainte logistique, offrent un outil alternatif pour étudier de potentiels mécanismes d’assemblage des communautés. Leur développement est toutefois limité par un manque de connaissances des mécanismes structurant les communautés benthiques. Dans le cadre de cette thèse, le premier chapitre du manuscrit tente une revue des outils de modélisation statistique et mécaniste utilisés dans l’étude des macroinvertébrés marins benthiques. Le but est d’identifier une technique permettant d’étudier la dynamique et le comportement de la biodiversité benthique d’une manière spatialement explicite, en utilisant des données déjà existantes. Même si l’implémentation d’un modèle mécaniste semble s’ajuster aux communautés benthiques, son utilisation nécessite la création d’un nombre limité d’entités avec un rôle fonctionnel clair. Le second chapitre du manuscrit utilise l’hypothèse des groupes émergents, afin de faire ça via une procédure objective et testable. Ce travail combine un jeu de données d’abondance de macroinvertébrés benthiques issu de l’estuaire de la Rance et une matrice de traits biologiques qui décrit le rôle de 240 espèces dans 7 mécanismes généraux d’assemblage des communautés. L’agrégation en 20 groupes fonctionnels est testée face aux postulats de l’hypothèse des groupes émergents. Les résultats généralement positifs supportent la capacité du groupement à reproduire la diversité fonctionnelle dans l’estuaire de la Rance. Un regard rapide sur les groupes renseigne également sur le rôle de quelques mécanismes dans le contrôle des communautés benthiques. Le manque de connaissances dans l’attribution des relations entre les composantes fonctionnelles dérivées précédemment reste important. Le troisième chapitre du manuscrit s’inscrit dans ce besoin, basé sur des théories écologiques qui prévoient l’existence de trade- offs fonctionnels opérant à grande et petite échelle. Les premiers représentent des processus de type filtre environnemental, alors que les deuxièmes impliquent des trade-offs dans les traits d’histoire de vie. Les associations de traits observées semblent en accord avec ces prédictions, appuyant la capacité de ces processus à façonner les communautés benthiques de l’estuaire de la Rance. Dans un premier temps, des éléments de théorie écologique sont associés à des dires d’experts et incorporées dans 2 modèles qualitatifs des 20 groupes fonctionnels. La stabilité de ces modèles illustre leur potentiel à constituer une représentation plausible du monde naturel. Leur structure pourrait offrir des indices sur la direction potentiellement prise par le système en réponse à des perturbations. Malgré l’intérêt du développement et de l’analyse de modèles qualitatifs, le but d’étudier la dynamique et le comportement spatialement explicite de la biodiversité ne peut être atteint que par un modèle avec ces mêmes caractéristiques. Le quatrième chapitre du manuscrit présente l’architecture d’un modèle individu-centré, en mettant l’accent sur le transfert des règles d’interactions des modèles qualitatifs vers un cadre dynamique et
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