Mapping global biodiversity, profiling invasive species and developing a global index of biodiversity change based on taxonomic, functional and phylogenetic facets of freshwater fish biodiversity Guohuan Su To cite this version: Guohuan Su. Mapping global biodiversity, profiling invasive species and developing a global index of biodiversity change based on taxonomic, functional and phylogenetic facets of freshwater fish biodi- versity. Ecosystems. Université Paul Sabatier - Toulouse III, 2020. English. NNT : 2020TOU30292. tel-03332349 HAL Id: tel-03332349 https://tel.archives-ouvertes.fr/tel-03332349 Submitted on 2 Sep 2021 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 En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par l'Université Toulouse 3 - Paul Sabatier Présentée et soutenue par Guohuan SU Le 2 décembre 2020 Cartographie de la biodiversité mondiale, profilage des espèces envahissantes et élaboration d'un indice global du changement de la biodiversité basé sur les facettes taxonomiques, fonctionnelles et phylogénétiques de la biodiversité des poissons d'eau douce Ecole doctorale : SEVAB - Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingenieries Spécialité : Ecologie, biodiversité et évolution Unité de recherche : EDB - Evolution et Diversité Biologique Thèse dirigée par Sébastien BROSSE et Sébastien VILLÉGER Jury M. Loïc PELLISSIER, Rapporteur M. Eric ROCHARD, Rapporteur M. Valeriano PARRAVICINI, Examinateur Mme Maud MOUCHET, Examinatrice M. Thierry OBERDORFF, Examinateur M. Sébastien BROSSE, Directeur de thèse M. Sébastien VILLÉGER, Co-directeur de thèse PhD Thesis Mapping global biodiversity, profiling invasive species and developing a global index of biodiversity change based on taxonomic, functional and phylogenetic facets of freshwater fish biodiversity Guohuan SU Jury composition Loïc PELLISSIER Professor Referee Eric ROCHARD Research Director Referee Valeriano PARRAVICINI Associate Professor Jury member Maud MOUCHET Associate Professor Jury member Thierry OBERDORFF Research Director Jury president Sébastien BROSSE Professor Supervisor Sébastien VILLÉGER CNRS researcher Co-supervisor Defence date: December 2, 2020 University of Toulouse Acknowledgements September 19th, 2016, I arrived at Toulouse and started my Ph.D. journey in the Lab EDB. Now, after four years, I am about to finish my Ph.D. thesis. I appreciate all of you who helped me in my life, especially during the past four years. Firstly, I would like to express my deepest gratitude to my supervisors, Prof. Sébastien Brosse, and Dr. Sébastien Villéger. I still feel so lucky to have sent you the first email to ask for a Ph.D. position and finally got the opportunity to spend four years working with both of you so fantastic scientists. Thank you for your supervision, encouragement and patience, I won’t be able to finish my thesis without you. I am very grateful that Sébastien (B) always gave me the maximum freedom to conduct my work and encouraged and inspired me when I felt frustrated and depressed. Your profound knowledge of ichthyology and rigorous attitude towards science have deeply influenced me. Apart from this, I also learned a lot from you about how to work effectively and balance work and family. I wish one day I will become a gentle person and a great researcher like you. Sébastien (V) worked in another city, thus we communicated mostly via email or Zoom and met in person for only a few times, but I still gained a lot of support from you. Your enthusiasm for research, insightful ideas and expertise in functional diversity were indispensable parts for me to finish my Ph.D. project. And also thank you for giving me very useful R statistical and visualization books. I would like to thank all my jury members: Prof. Loïc Pellissier, Prof. Eric Rochard, Prof. Oberdorff Thierry, Dr. Valeriano Parravicini and Dr. Maud Mouchet. Your valuable comments, suggestions and discussions helped me improve my dissertation. I would like to thank my collaborators, Prof. Jun Xu, Dr. Pablo Tedesco, Dr. Maxime Logez, Dr. Shengli Tao, Dr. Aurele Toussaint. Thank you for your contribution in data collection, statistical support, and valuable ideas for our collaborative articles. I would like to acknowledge the China Scholarship Council (CSC) for the financial support, without the funding, I would not be able to pursuit my Ph.D. study in this beautiful city and the wonderful ecological research institute. Special thanks to Prof. Sovan Lek and Sithan Lek. Thank you very much for your kindness and hospitality. It was really a wonderful memory to travel with you along the coast of the Mediterranean Sea and Spain. I will also miss the sunshine afternoon when we had dinner together under the cherry tree in your yard, the delicious meals you made and many kinds of sweet fruits we picked up. I would like to thank all my colleagues in lab EDB: Dominique, Elisabeth, Florence, Céline, Kevin, Jade, Isabel, Shiyu, Xianghong, Tao, Iris, Quentin…. I am very grateful for your kind help when I encountered various problems in the lab. I would like to thank my Chinese fellows in Toulouse, Hui, Manlu, Yin, Su, Haoyu…. Together we traveled and visited lots of beautiful scenes across Europe. I will also miss those freezing but exciting winters when we went skiing in the Pyrenees. Thank you for making my life full of joy and passion. Last but not least, I would like to thank my parents, sister and brother. Wherever I am, your warming encouragements and unconditional supports are my greatest power to overcome any obstacles. I also would like to thank my girlfriend, Yue. You slipped into my life at the end of the second year of my Ph.D. and also into my heart. You make my life colorful and I will do my best to make a bright future for us. 谨以此文感谢那些曾帮助过鼓励过我的人们. Merci, tout le monde! 路漫漫其修远兮，吾将上下而求索. Guohuan Su, Toulouse ABSTRACT ABSTRACT Biodiversity is a multifaceted concept that includes three main components, namely taxonomic, phylogenetic and functional diversity. Biogeographical studies have paid more attention to the first two facets while the patterns and drivers of functional diversity and their changes because of global change remains largely unknown at the global scale. These knowledge gaps are especially large for freshwater fishes, because they not only account for a quarter of vertebrates and support the functioning and stability of ecosystems, but are also one the most threatened vertebrates groups in the world. Thus this thesis aims to improve the understanding of the functional diversity of global freshwater fishes and bridge the gap between taxonomic, functional and phylogenetic facets to evaluate the impacts of human activities on the multifaceted biodiversity of global fishes. Towards this aim, we first built a trait database describing the morphology of 10 600 species occurring in over 2 400 river basins all over the six terrestrial realms. First, we assessed the distributions of the morphological traits within the fauna of each realm. We revealed that fish morphological traits are different between realms and that morphologically extreme species are distributed in all realms. Second, using a multi-traits approach at the basin scale we found that the historical functional diversities have been shaped by habitat, energy and history-related variables. Third, we demonstrated that morphology differs between species that have never been introduced species and those that were introduced and those that were even established. Last, using a novel cumulative index combining changes in six facets of biodiversity we found that human activities have markedly affected fish biodiversity in more than half of the world river (52.8%, 1 297 rivers). Those biodiversity changes were primarily due to alterations of water connectivity and introductions of non-native species. This work underlined the potential of morphological features in the study of global freshwater fish functional diversity, and the combination of functional phylogenetic and taxonomic features in a novel multifaceted biodiversity change index will constitute a useful tool for biological conservation. 3 RESUME RESUME La biodiversité est un concept à multiples facettes qui comprend trois composantes principales, à savoir la diversité taxonomique, phylogénétique et fonctionnelle. Les études biogéographiques ont jusqu’à présent accordé plus d'attention aux deux premières facettes tandis que les déterminants de la diversité fonctionnelle et ses changements sous l’effet de l’anthropisation restent largement inconnus à l'échelle du globe. Ces lacunes sont particulièrement importantes pour les poissons d'eau douce, car ils représentent non seulement un quart des vertébrés et soutiennent le fonctionnement et la stabilité des écosystèmes, mais sont également l'un des groupes de vertébrés les plus menacés au monde. Ainsi, l'objectif de cette thèse est d'améliorer la compréhension de la diversité fonctionnelle des poissons d'eau douce du globe et de combler le fossé entre les facettes taxonomiques, fonctionnelles