Evolution of the wild tomato species Solarium chilense: demography and natural selection Dissertation an der Fakultat fur Biologie der Ludwig-Maximilians-Universitat Miinchen vorgelegt von Katharina Barbara Bondel aus Rinteln Miinchen, April 2014 http://d-nb.info/1058423304 Contents Contents 1 Summary 3 Zusammenfassung 5 Abbreviations 7 List of figures 9 List of tables 11 CHAPTER 1: INTRODUCTION 15 1.1 Adaptation in plants 15 1.2 Wild tomatoes as a model system to study evolution 16 1.2.1 Natural habitat and adaptations 16 1.2.2 Genomic features, mating system, and genetic variation 17 1.2.3 The cultivated tomato 17 1.3 Abiotic stress response in plants 18 1.4 Molecular signatures of local adaptation to abiotic stresses in wild tomato species 20 1.5 The aim of this study 22 CHAPTER 2: MATERIAL AND METHODS 25 2.1 Sequence evolution in Solarium chilense 25 2.1.1 Plant material and plant growing 25 2.1.2 Choice of genes and primer design 28 2.1.3 Sequencing approach for Solanum chilense 30 2.1.4 Sequencing of the outgroup species S. ochranthum and S. lycopersicoides 32 2.1.5 Sequence data analyses 32 2.1.5.1 Data assembly 32 2.1.5.2 Summary statistics of the whole data set 34 2.1.5.3 Regressions and correlations 35 2.1.5.4 Population differentiation and isolation by distance 35 2.1.5.5 Detecting selection in Solanum chilense 36 2.1.5.6 Analysis of the consensus sequence data set 37 2.2 Salt stress experiment 39 CHAPTER 3: RESULTS 41 3.1 Sequence data 41 1 3.2 Demographic history of Solanum chilense 42 3.2.1 Within population levels of variation and population averages of Tajima's D 42 3.2.2 Population differentiation and isolation by distance 45 3.2.3 Genetic differentiation and divergence from other Solanaceae species 49 3.3 Genes under selection in Solanum chilense 52 3.3.1 Candidate genes vs. reference genes 52 3.3.2 Regulatory genes vs. functional genes 54 3.3.3 Detection of local adaptation 57 3.3.4 Single gene evolutionary histories 66 3.4 Analysis of the consensus sequence data set 75 3.4.1 Gene evolution on the species level 75 3.4.2 Phylogenetic analyses 78 3.4.3 Footprints of selection 80 3.5 Differential behaviour after application of salt 82 CHAPTER 4: DISCUSSION 83 4.1 Evaluation of the data generation 83 4.2 Demographic history of Solanum chilense 85 4.2.1 North-south cline indicates migration from north to south 85 4.2.2 Isolation by distance and genetic differentiation define population groups 87 4.3 Local adaptation in Solanum chilense 90 4.3.1 Gene evolution on the species level 90 4.3.2 Different methods to detect outliers in the data set 92 4.3.3 Signatures of selection in the coastal populations 95 4.3.4 Adaptation in high altitude populations 99 4.3.5 Signatures of balancing selection in abiotic stress genes 100 4.4 The utility of consensus sequences in molecular evolution 103 4.5 Conclusion and outlook 105 APPENDIX A: Material and methods 107 APPENDIX B: Results 115 Bibliography 165 Acknowledgements 175 Curriculum vitae 177 2 .