Speed of adaptation of forest trees to climate change

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Table of contents

Introduction
1.Speed of adaptation of forest trees to climate change
2.Overview of the concept of local adaptation
3.Main approaches by which to demonstrate local adaption
3.1.Approaches to searching for signs of selection among populations
3.2.Approaches for searching for the signal of selection within a population
4.Disentangling the role of demography and adaptation in the interpretation of patterns of local adaptation
5.Latitudinal versus altitudinal gradient as models for investigating local adaptation
6.Objectives of the thesis
Chapter 1. Species and sites
1.Fagus sylvatica
1.1.Phylogenetic origin
1.2.The post-glacial distribution of Fagus sylvatica
1.3.Main physiological and ecological properties
1.4.Bud burst phenology
1.5.The genome of F. sylvatica
2.Mont Ventoux
3.The history of Fagus sylvatica on Mont Ventoux
Chapter 2. Candidate genes selection and SNP discovery
1.Context
2.Abstract
3.Introduction
4.Material and methods
4.1.Plant material
4.2.EST databases and annotation
4.3.Candidate gene selection
4.4.Primer design and gene amplification
4.5.Candidate gene sequencing
4.6.Data analysis
4.6.1.Phase reconstruction
4.6.2.Nucleotide diversity, LD patterns and recombination
5.Results
5.1.Gene selection, amplification and sequencing
5.2.Genomic diversity
5.3.Linkage disequilibrium (LD)
6.Discussion
7.Appendices
Chapter 3. Detection of loci under selection in Fagus Sylvatica along an altitudinal gradient: an outlier experimental approach
1.Context
2.Abstract
3.Introduction
4.Materials and methods
4.1.Study species and site
4.2.Candidate gene selection, sequencing and SNP validation
4.3.Genetic diversity, differentiation and linkage disequilibrium at candidate genes
4.4.SSR data
4.5.Frequentist outlier approach
4.6.Bayesian outlier approach
4.7.Relation between outlier SNP and traits
5.Results
5.1.Genetic diversity and differentiation at SNP and SSR markers
5.2.Frequentist outlier approach
5.3.Bayesian outlier approach
5.4.Patterns of between-population correlations for SNP pairs
5.5.Relation between outlier SNPs and functional traits
6.Discussion
7.References
8.Appendices
Chapter 4. Interaction between selection and gene flow in the building of genetic differentiation along an altitudinal gradient: lessons from an Eco-Physio-Demogenetic simulation model
1.Context
2.Introduction
3.Materials and Methods
3.1.The model and the simulated data sets
3.2.Measures of population differentiation
3.3.Patterns of genotypic and allelic frequencies across elevation
3.4.FST -based outlier approaches
3.5.Patterns of covariance among populations
4.Results
4.1.Patterns of genetic differentiation for the trait (FcritBB), the QTLs and the neutral loci
4.2.FST -based genome scan between populations Pop2 and Pop3
4.3.Patterns of genotypic and allelic frequencies across elevation
4.4.Inter-genic allelic correlation among populations Pop2 and Pop3
5.Discussion
5.1.Comparison with theoretical expectations
5.2.Global performance of FST -based outlier approaches
5.3.Performance of methods that are based on clines of genotypic frequencies
5.4.Performance of the between-population component of intergenic linkage disequilibrium (Zg)
6.Conclusion