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Table of contents
INTRODUCTION – Evolution in Amazonia
1. Short overview of the Amazonian rainforest
2. The building of biodiversity in Amazonia
3. The maintenance of diversity in Amazonia: a subtle combination of chance and determinism
4. Spatial heterogeneity in the Amazonian rainforest
5. Tree species model, research questions and study sites
PART 1 – Molecular evolution: population genetics and genomics
1. Population evolution
2. Population differentiation: the complex interplay between gene flow, selection, and drift.
3. Neutral differentiation
4. Adaptive differentiation
5. Next generation sequencing / genotyping and new opportunities
PART II – Phenotypic evolution and quantitative genetics
1. Causes of phenotypic variation
2. Phenotypic evolution in populations
3. Phenotypic differentiation
DISCUSSION
1. Neutralism and adaptation in Eperua falcata
2. Open questions and perspectives
3. Importance of assessing genetic diversity in a changing world
PhD RESULTS & DEVELOPMENT OF BIOINFORMATIC TOOLS
Article n°1 Molecular divergence in tropical tree populations occupying environmental mosaics
Article n° 2 Genome scan reveals fine-scale genetic structure and suggests highly local adaptation in a Neotropical tree species (Eperua falcata, Fabaceae) Bioinformatic tools ‘
Rngs’: A suite of R functions to easily deal with next-generation (454-)sequencing data and post-process assembly and annotation results.
1. Introduction to bioinformatics
2. Short description of ‘Rngs’
3. Short overview of the functions
4. Detailed description of the functions
Article n°3 High-throughput transcriptome sequencing and polymorphism discovery in four Neotropical tree species.
Article n°4 Highly local environmental variability promotes intra-population divergence of quantitative traits: an example from tropical rainforest trees
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
Preliminary results Reciprocal transplants
BIBLIOGRAPHY
