Genetic structure, phylogeography, adaptive variation and speciation in the tropical tree genus Symphonia

Abstract

Resumen 1. Introduction 1.1. Fine-scale spatial genetic structure and its drivers 1.2. Large-scale genetic structure, demographic history and adaptive evolution 1.3. Challenges to evolutionary research in tropical rainforest trees 1.4. Study group: the tropical tree genus Symphonia L. f. 1.4.1. Symphonia globulifera 1.4.2. Malagasy Symphonia 2. Objectives of the thesis 3. Materials and Methods 3.1. Study sites, molecular markers and other related information 3.1.1. Fine-scale spatial genetic structure in S. globulifera (Study I) Study sites and plant material Molecular markers 3.1.2. Large-scale genetic structure in S. globulifera, demographic history and adaptive evolution (Study II, parts 1 & 2)3.1.2.1. Spatial genetic structure of S. globulifera across continents Study sites and plant material Molecular markers 3.1.2.2. Local adaptation of S. globulifera at continental scale in Africa Study sites and molecular markers Environmental Data Selection 3.1.3. Genetic structure within the genus Symphonia in Madagascar (Study III) Study sites and plant material Molecular markers 3.2. Data analysis 3.2.1. Fine-scale spatial genetic structure in S. globulifera (Study I) Genetic diversity Test and quantification of FSGS Spatial genetic heterogeneity and its causes 3.2.2. Large-scale genetic structure in S. globulifera, demographic history and adaptive evolution (Study II) 3.2.2.1. Spatial genetic structure of S. globulifera across continents (Study II, part I) Inference of improved genotypes and gene pool delimitation Genetic diversity Phylogeographic history 3.2.2.2. Local adaptation of S. globulifera at continental scale in Africa (Study II, part 2) Outlier tests Gene Annotation 3.2.3. Genetic structure within the genus Symphonia in Madagascar (Study III) Genome size estimation and ploidy level inference using flow cytometry Gene pool delimitation and phylogenetic relationshipsCongruence of genetic and morphological species delimitation 4. Results 4.1. Fine-scale spatial genetic structure in S. globulifera (Study I) Genetic diversity Fine scale spatial genetic structure (FSGS) Spatial genetic heterogeneity and its causes 4.2. Large-scale genetic structure in S. globulifera, demographic history and adaptive evolution (Study II) 4.2.1. Spatial genetic structure of S. globulifera across continents (Study II, part 1) Inference of genotypes and gene pool delimitation Genetic diversity Genetic distance Phylogeographic history 4.2.2. Local adaptation of S. globulifera at continental scale in Africa (Study II, part 2) Synthesis of Outlier Tests 4.3. Genetic structure within the genus Symphonia in Madagascar (Study III) SNP genotyping and inference of ploidy Ploidy levels inferred from nuclear genome size data and SNP genotypes Genetic structure of Symphonia in Madagascar Phylogenetic relationships Congruence of genetic and morphological species delimitation 5. Discussion 5.1. Fine-scale spatial genetic structure in S. globulifera (Study I) Methodological considerations Biotic and abiotic determinants of within-population spati...