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Diversity and Evolution in Tropical Rainforest Trees: Example of Eperua Falcata in French Guiana Louise Brousseau

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Diversity and Evolution in Tropical Rainforest Trees: Example of Eperua Falcata in French Guiana Louise Brousseau Diversity and Evolution in tropical rainforest trees: example of Eperua falcata in French Guiana Louise Brousseau To cite this version: Louise Brousseau. Diversity and Evolution in tropical rainforest trees: example of Eperua fal- cata in French Guiana. Biodiversity and Ecology. Université de Lorraine, 2013. English. NNT : 2013LORR0188. tel-00967318 HAL Id: tel-00967318 https://tel.archives-ouvertes.fr/tel-00967318 Submitted on 28 Mar 2014 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. Collegium Sciences & Technologies Ecole Doctorale RP2E Thèse présentée pour l'obtention du titre de Docteur de l'Université de Lorraine en Biologie Végétale et Forestière par Louise BROUSSEAU Diversité et Evolution des Arbres de Forêt Tropicale Humide: Exemple d’Eperua falcata en Guyane française. Soutenance publique le 10 Décembre de l’an 2013 Membres du jury : Rapporteurs : Sophie KARRENBERG Professeur associé, Université d’Uppsala, Suède Santiago GONZALEZ-MARTINEZ Directeur de recherche, INIA Madrid, Spain Examinateurs : François LEFEVRE Directeur de recherche, INRA Avignon, France Benoît PUJOL Chargé de recherche, CNRS Toulouse, France Sylvain DELZON Chargé de recherche, INRA Bordeaux, France Ivan SCOTTI (directeur de thèse) Directeur de recherche, INRA Kourou, Guyane Erwin DREYER (directeur de thèse) Directeur de recherche, INRA Nancy, France ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ---------------------------------- INRA, UMR EEF (« Ecologie et Ecophysiologie Forestières », Champenoux, France) & INRA, UMR EcoFoG (« Ecologie des Forêts de Guyane », Kourou, Guyane française) 0 1 Foreword .................................................................................................................................... 4 Acknowledgements ................................................................................................................... 6 SYNTHESIS ...................................................................................................................... 10 INTRODUCTION - Evolution in Amazonia ...................................................................... 12 1. Short overview of the Amazonian rainforest .............................................................. 12 2. The building of biodiversity in Amazonia .................................................................. 15 3. The maintenance of diversity in Amazonia: a subtle combination of chance and determinism ...................................................................................................................... 22 4. Spatial heterogeneity in the Amazonian rainforest .................................................... 24 5. Tree species model, research questions and study sites .............................................. 32 PART 1 - Molecular evolution: population genetics and genomics ...................................... 38 1. Population evolution ..................................................................................................... 38 2. Population differentiation: the complex interplay between gene flow, selection, and drift. ................................................................................................................................... 50 3. Neutral differentiation .................................................................................................. 52 4. Adaptive differentiation .............................................................................................. 60 5. Next generation sequencing / genotyping and new opportunities ........................... 74 PART II - Phenotypic evolution and quantitative genetics .................................................. 81 1. Causes of phenotypic variation .................................................................................... 81 2. Phenotypic evolution in populations ........................................................................... 91 3. Phenotypic differentiation ........................................................................................... 94 DISCUSSION ....................................................................................................................... 105 1. Neutralism and adaptation in Eperua falcata .............................................................. 105 2. Open questions and perspectives ................................................................................ 111 3. Importance of assessing genetic diversity in a changing world ................................ 113 PhD RESULTS & DEVELOPMENT OF BIOINFORMATIC TOOLS....................... 117 Article n°1 • Molecular divergence in tropical tree populations occupying environmental mosaics ..................................................................................................................................... 119 2 Article n° 2 • Genome scan reveals fine-scale genetic structure and suggests highly local adaptation in a Neotropical tree species (Eperua falcata, Fabaceae) .................................... 147 Bioinformatic tools ­ ‘Rngs’: A suite of R functions to easily deal with next-generation (454-)sequencing data and post-process assembly and annotation results. ......................... 171 1. Introduction to bioinformatics .................................................................................... 171 2. Short description of ‘Rngs’ ......................................................................................... 172 3. Short overview of the functions .................................................................................. 173 4. Detailed description of the functions ......................................................................... 173 Article n°3 • High-throughput transcriptome sequencing and polymorphism discovery in four Neotropical tree species. ................................................................................................ 179 Article n°4 • Highly local environmental variability promotes intra-population divergence of quantitative traits: an example from tropical rainforest trees ........................................ 197 Article n°5 • Local adaptation in tropical rainforest trees: response of E. falcata (Fabaceae) seedling populations from contrasted habitats to drought and to water-logging ............... 227 Preliminary results • Reciprocal transplants ........................................................................ 244 BIBLIOGRAPHY ............................................................................................................. 261 3 Foreword This PhD was supported by a CJS INRA leading to a two years post-doctoral contract. My research work was carried out in two INRA mixt unit research “EcoFog” (Ecology of Forests of French Guiana) and “EEF” (Forest Ecology and Ecophysiology) and supported by MEDD ECOFOR ‘Ecosystèmes tropicaux’, PO-FEDER ‘ENERGIRAVI’ and ‘CEBA’ (Labex) research programs. This manuscript was written as a global synthesis containing the state of the art, the main results and a general discussion. I tried to link ecology and population evolution in a global ‘ecological genetics’ approach. Particular theoretical notion and methods were included into ‘green’ and ‘purple’ boxes respectively. A synthetic summary of each main result was integrated in the synthesis through a topic sentence, a short description of the experiment and the main figures. Complete methods and results are described in research articles, and given a part from the global synthesis. For more readability, figures and tables were included in the main text of research articles rather than giving them a part. For more simplicity and to avoid redundancies, I merged the bibliographies of synthesis and research papers into a single bibliography. 4 5 Acknowledgements Je remercie chaleureusement toutes les personnes qui m’ont aidée, accompagnée, soutenue et participé à l’aboutissement de cette thèse. Je tiens cependant à addresser des remerciements tout particuliers … A mes directeurs de thèse, Ivan Scotti et Erwin Dreyer, Qui ont su guider ma réflexion pendant ces trois années, apprivoiser mon énergie et apaiser mes craintes. Ivan, je te remercie de m’avoir transmis tes savoirs avec passion, et de m’avoir offert un enseignement d’une grande qualité scientifique. Je te remercie aussi de l’habileté avec laquelle tu as su m’octroyer une immense liberté, tout en sachant canaliser mes ambitions. Je te remercie Erwin de ton soutien pendant ces trois années de thèse, et de tes précieux conseils en écophysiologie. Je te remercie aussi d’avoir pris le temps de te rendre en Guyane chaque année pour suivre ma thèse et de m’avoir accompagnée chaque fois sur le terrain ! ∞ A Damien Bonal, Pour m’avoir gentiment confié ses données issues des expérimentations de « common garden » et « traitements hydriques » qui auront occupé une part importante de ma thèse et m’ont permis de croiser les approches
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