Comparative and population transcriptomics of Daphnia galeata Dissertation submitted with the aim of achieving a doctoral degree at the Faculty of Mathematics, Informatics and Natural Sciences Department of Biology Universität Hamburg Submitted by Suda Parimala Ravindran July 2018 i Thesis Evaluators: 1. Prof. Dr. Mathilde Cordellier 2. Dr. Luisa Orsini ii “Learning gives creativity Creativity leads to thinking Thinking provides knowledge Knowledge makes you great.” ― A.P.J. Abdul Kalam iii To Daddy and Amma … for their innumerable sacrifices, unconditional love, encouragement and trust since my existence iv v Table of Contents List of Figures ...................................................................................................................................... viii List of Tables ......................................................................................................................................... ix List of abbreviations .............................................................................................................................. x Abstract .................................................................................................................................................. 1 I. General introduction .......................................................................................................................... 3 I-1 Genetic versus plastic adaptive responses .................................................................................. 4 I-1.1 Genetic variation .................................................................................................................... 4 I-1.2 Phenotypic variation ........................................................................................................... 11 I-2 Assessing the genetic basis of local adaptation ....................................................................... 13 I-2.1 Expression-based divergence .............................................................................................. 13 I-2.2 Sequence-based divergence ................................................................................................ 13 I-3 Linking genotypes and phenotypes ........................................................................................... 14 I-4 Daphnia as a model organism .................................................................................................. 15 I-4.1 Daphnia Genomics .............................................................................................................. 16 I-4.2 Local adaptation in Daphnia .............................................................................................. 17 I-4.3 Inducible defences in Daphnia............................................................................................ 19 Thesis Outline ...................................................................................................................................... 21 Chapter 1: Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations ............................................................................................... 23 Introduction ..................................................................................................................................... 24 Methods ........................................................................................................................................... 28 Results .............................................................................................................................................. 36 Discussion ......................................................................................................................................... 45 Chapter 2: DaphniaStressdb: Taking advantage of a decade of Daphnia ‘-omics’ data for gene annotation ........................................................................................................................................... 56 Introduction ..................................................................................................................................... 57 Methods ........................................................................................................................................... 59 Results and Discussion ..................................................................................................................... 62 Conclusion ........................................................................................................................................ 71 vi Chapter 3: An environment-dependent genotype-phenotype association in European Daphnia galeata.................................................................................................................................................. 73 Introduction ..................................................................................................................................... 74 Methods ........................................................................................................................................... 77 Results and discussion ..................................................................................................................... 82 Limitations and conclusions............................................................................................................ 88 D. General discussion .......................................................................................................................... 93 D.1 Local adaptation in Daphnia galeata ...................................................................................... 94 D.1a Genetic drift ......................................................................................................................... 94 D.1b Natural selection ................................................................................................................. 95 D.1c Dispersal and gene flow ...................................................................................................... 96 D.2 Genotype-phenotype associations........................................................................................... 98 D.3 Functional annotation ............................................................................................................ 100 Future directions ............................................................................................................................... 101 Conclusions ........................................................................................................................................ 102 Appendix for Chapter 1 ..................................................................................................................... 104 Appendix for Chapter 3..................................................................................................................... 107 Author Contributions ........................................................................................................................ 115 Eidesstattliche Versicherung ........................................................................................................... 116 Acknowledgements .......................................................................................................................... 117 References .......................................................................................................................................... 118 vii List of Figures Figure 1: Consequences of variation at different levels........................................................... 6 Figure 2: Life cycle of Daphnia and its ecological interactors. .............................................. 18 Figure 3: Waterfleas, Daphnia galeata, Photo: Mathilde Cordellier .................................. 26 Figure 4: Gene expression patterns. ........................................................................................... 38 Figure 5: SNP patterns and heterozygosity. .............................................................................. 41 Figure 6: Flow diagram representing the proportion of transcripts that are candidates for local adaptation at the regulatory and sequence level. ......................................... 43 Figure 7: Assessment of assembly artefacts and inparalogs. ............................................... 46 Figure 8:Cluster dendrogram of transcripts for the reference network in Daphnia galeata, with dissimilarity based on the topological overlap matrices (TOM)......... 47 Figure 9: Workflow of Daphnia-specific gene expression meta-analysis. ....................... 61 Figure 10: Literature statistics for meta-analysis. ................................................................... 63 Figure 11a-c: Pie charts showing the percentage of genes associated to a stressor in the literature database. ................................................................................................................ 65 Figure 12: Circular and bubble plot showing the number of genes associated to one or more stressors in D. magna. ................................................................................................. 66 Figure 13: Circular and bubble plot showing the number of genes associated to one or more stressors in D. pulex. ...................................................................................................