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Agroparistech N°: 2017AGPT0007 Doctorat AgroParisTech T H È S E pour obtenir le grade de docteur délivré par L’Institut des Sciences et Industries du Vivant et de l’Environnement (AgroParisTech) Spécialité : Ecosystèmes et Sciences Agronomiques présentée et soutenue publiquement par Ruksan BOSE le 26 Avril 2017 Influence of past and present environment on the ecology and biogeography of tree species in the Western Ghats biodiversity hotspot Directeur de thèse : Raphaël Pélissier Co-diréction de la thèse : François MUNOZ Jury M. Andréas PRINZING, Professeur, Université de Rennes 1, UMR ECOBIO, Rennes Président M. Dario DE FRANCESCHI, Maître de Conférences, MNHN, UMR PACE, Paris Rapporteur Mme. Priya DAVIDAR, Professeur, Dept.of Ecology & Environmental Sciences, Examinatrice Pondicherry University, India M. Jean-Yves BARNAGAUD, Maître de Conférences, EPHE, UMR CEFE, Montpellier Examinateur M. Raphaël PELISSIER DR IRD, UMR AMAP, Montpellier Co-directeur M. François MUNOZ Maître de Conférences, Université de Montpellier, HoD Ecology Dept., Co-directeur Institut Français de Pondichéry, India AgroParisTech Unité Mixte de Recherche AMAP, TA A-51 / PS2 Bd de la Lironde, 34 398 Montpellier cedex 5, FRANCE 2 3 Acknowledgements Above all, I thank my thesis directors Raphael Pélissier and François Munoz, who were consistently there for me, navigating my journey towards natural treasures untold, from beginning to end. I thank them for guiding me, supporting me, and for inspiring me. I thank them for their invaluable inputs and scientific insights into my work, for always being approachable and making themselves available despite busy schedules and other students to supervise. Most importantly I thank them for giving me just enough, for opening the door to possibilities just wide enough, to allow me to find my own path. I am also grateful for their infinite patience as I moved between France and India, and later Cameroon; for always promptly responding to my mails and need for long-distance skype conversations; for their meticulous reading of and comments on drafts for publication; for helping me with the formalities and costs involved not only in a thesis but also in moving from country to country. I was lucky not only in my thesis directors, I also found a suitable habitat in which my thesis could flourish in different continents: IFP in Pondicherry, AMAP in Montpellier, ENS in Yaoundé, ULB in Brussels. The varying climatic conditions sometimes took some adapting to, but my experience was greatly facilitated by biotic interactions in each site. I am especially grateful to the IFP technical staff and botanists who contributed over years to data collection in the Western Ghats. I thank Dr. Ramesh, Dr. Ayyappan, Aravajy and Ravi Barathan from whom I learned much at IFP and in the field. I would like to specifically thank Professor Bonaventure Sonké at ENS, Yaoundé and Dr. Tariq Stévart at ULB, Brussels for accommodating me in their laboratories and making me feel a part of their teams. I am indebted to members of my thesis committees and the jury, especially Dr. Andreas Prinzing and Dr. Dario DeFranceschi for their encouragement and useful comments on the final manuscript. Those who helped me in my evolution from student to researcher are too numerous to name individually here, but I thank the researchers, librarians, co-PhD students and staff at AMAP, IFP, ENS and ULB for their welcome, intellectual support and stimulation; especially Jimmy, Pol and Diane for their help during initial encounters with R and spatial analyses as well as for their emotional support. For contributing to the environmental bonheur component of my PhD, I have my house-mates Sandra, Maud, Alphonsina, Demian and Alexandra, Mythri and other friends in Pondicherry and Montpellier, friends from Montpellier in Pondy, and friends from Pondy in Montpellier to thank. I am similarly indebted to Felix, Natacha, Martha and the Kalims in Yaoundé. A special thanks to Manolita Alonso for kindly hosting me in Montpellier for my thesis defense. How does one thank one’s family? How to account now for the daily gifts that went unrecognized? My aunt Ratna Sen, my sisters Nilüfer and Tara, and my niece and bringer of unending joy, Isabel, gave me support and love through this time. My parents and uncles Jethu and Pishe who are no longer with us, left their imprint by giving me what it takes to want to do a PhD and to succeed in it. BPG is my eternal support base. My second family in Belgium encouraged me, fed me and cheered me through the final days of writing, grand merci to Catherine and Phillippe, the Deblauwes and the Lethés. I have no words to express my gratitude to my partner Vincent Deblauwe for standing by me in all aspects of the exciting and challenging peregrination that a PhD represents, for I could not have done it without him. 4 5 Table of Contents RESUME DETAILLE EN FRANÇAIS 7 PART I GENERAL INTRODUCTION 25 A. BACKGROUND: HISTORICAL PERSPECTIVE 31 1. ECOLOGY AND BIOGEOGRAPHY: ‘DUEL’ VIEWS 31 2. ECOLOGICAL NICHE, EVOLUTIONARY DYNAMICS 34 B. BACKGROUND: THE REGIONAL SCALE 37 1. MEETING IN THE MIDDLE 37 2. BRIDGING THE GAP: METHODOLOGICAL APPROACHES 40 3. HYPOTHESES AND EXPECTATIONS 44 MATERIAL AND METHODS 46 A. PHYSICAL AND HISTORICAL CONTEXT: WESTERN GHATS OF INDIA 46 1. TOPOGRAPHIC AND HABITAT HETEROGENEITY 47 2. DYNAMIC BIOGEOGRAPHICAL HISTORY 48 3. ENDEMISM AND DIOECY IN THE WESTERN GHATS 51 B. THE DATA 52 1. QUANTIFYING PAST AND PRESENT ENVIRONMENTAL CONDITIONS 52 2. VARIATION IN FLORISTIC COMPOSITION ALONG ENVIRONMENTAL GRADIENTS 57 3. PHYLOGENETIC DATA 62 BIBLIOGRAPHY 63 PART II CHAPTER 1 PAST POTENTIAL HABITATS SHED LIGHT ON THE BIOGEOGRAPHY OF ENDEMIC TREE SPECIES OF THE WESTERN GHATS BIODIVERSITY HOTSPOT, SOUTH INDIA (JOURNAL OF BIOGEOGRAPHY) 71 CHAPTER 2 PHYLOGENETIC DIVERSITY IN THE WESTERN GHATS BIODIVERSITY HOTSPOT REFLECTS ENVIRONMENTAL FILTERING AND PAST NICHE DIVERSIFICATION OF TREES 93 CHAPTER 3 ROLE OF DIOECY IN THE ECOLOGICAL AND EVOLUTIONARY DYNAMICS OF TREES IN THE WESTERN GHATS: A LEGACY OF ARIDIFICATION? 117 GENERAL DISCUSSION AND CONCLUSION 143 1. OVERVIEW 144 2. THE STORY THAT CONGENERIC ENDEMICS TOLD: NICHE LABILITY 147 3. CONSERVATION OF ANCESTRAL PREFERENCES IN SOUTHERN REFUGIA 149 4. MACROEVOLUTIONARY CONTINGENCY 150 5. LIMITATIONS OPEN PERSPECTIVES 155 6. IMPLICATION FOR CONSERVATION 159 BIBLIOGRAPHY 161 ANNEXE 1 164 ANNEXE 2 169 6 RESUME DETAILLE EN FRANÇAIS 7 INTRODUCTION L'organisation de la biodiversité dans l'espace et le temps est déterminée par un mélange complexe de processus écologiques et évolutifs et pourrait refléter l’interaction de l'histoire climatique, biogéographique et géologique (Ricklefs, 2007; Harrison & Noss, 2017). Déchiffrer ces influences entremêlées est essentiel pour comprendre les questions fondamentales concernant la façon dont les espèces sont actuellement distribuées et rassemblées dans les communautés, et comment la biodiversité est produite, maintenue et façonnée dans le temps. Bien que l’attention des recherches ait été focalisée sur les processus écologiques actuels, des études récentes indiquent l'importance des processus évolutifs pour expliquer les patrons de biodiversité à travers les échelles spatiales. Les théories historiques (Ricklefs, 1987), surtout en ce qui concerne l'histoire du climat (Normand et al., 2011; Svenning et al., 2015), montrent comment les distributions contemporaines reflètent toujours l’héritage des environnements passés. Les processus géologiques et évolutifs tels que les événements de vicariance ou la variation des taux de diversification et d'extinction, ont également des effets durables sur les distributions actuelles d'espèces et leur assemblage dans les communautés (Luebert & Weigend, 2014; Sanín et al., 2016). Synthétiser comment les processus évolutifs, la contingence historique et les facteurs écologiques contemporains façonnent conjointement la répartition et l'accumulation d'espèces au sein des régions est une avenue de recherche émergente (Fine, 2015). Les progrès dans la modélisation de la distribution des espèces (SDM pour Species Distribution Model) ont conduit à étudier les limites historiques des distributions et la dynamique des habitats passés. Par exemple, les SDMs basés sur des occurrences passées et actuelles d'espèces ont été proposés pour obtenir des informations sur les processus biogéographiques tels que la contraction et l'expansion de l’aire de distribution des espèces suite aux changements de l’environnement (Svenning et al., 2011). Deuxièmement, l'analyse de la structure phylogénétique des assemblages d'espèces ajoute la dimension temporelle nécessaire pour aborder l'influence de la dynamique évolutive et biogéographique qui vient s’ajouter aux facteurs contemporains. La distance évolutive séparant les espèces peut être utilisée pour déchiffrer les processus d'assemblage écologique (Webb et al., 2002). Peut-être plus important encore, cette information peut être utilisée pour identifier les particularités macro-évolutives des habitats, les lignées associées à ces habitats, et les communautés crées à partir des lignées existantes (Gerhold et al., 2015). Enfin, le domaine émergent de la modélisation phyloclimatique, combine des SDM et des analyses phylogénétiques pour étudier, par exemple, l'héritabilité des préférences de niche climatique et la reconstruction des niches ancestrales (Yesson & Culham, 2006; Heibl & Calenge, 2013). Les forêts tropicales ont été la scène de grands événements évolutifs et biogéographiques, et sont parmi les écosystèmes les plus
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