EVOLUTIONARY GENOMICS OF A PLASTIC LIFE HISTORY TRAIT: GALAXIAS MACULATUS AMPHIDROMOUS AND RESIDENT POPULATIONS by María Lisette Delgado Aquije Submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Dalhousie University Halifax, Nova Scotia August 2021 Dalhousie University is located in Mi'kma'ki, the ancestral and unceded territory of the Mi'kmaq. We are all Treaty people. © Copyright by María Lisette Delgado Aquije, 2021 I dedicate this work to my parents, María and José, my brothers JR and Eduardo for their unconditional love and support and for always encouraging me to pursue my dreams, and to my grandparents Victoria, Estela, Jesús, and Pepe whose example of perseverance and hard work allowed me to reach this point. ii TABLE OF CONTENTS LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ........................................................................................................... ix ABSTRACT ...................................................................................................................... xii LIST OF ABBREVIATION USED ................................................................................ xiii ACKNOWLEDGMENTS ................................................................................................ xv CHAPTER 1. INTRODUCTION ....................................................................................... 1 1.1 Galaxias maculatus ................................................................................................... 3 1.2 Diadromous vs. resident G. maculatus populations .................................................. 5 CHAPTER 2. INVESTIGATING DIADROMY IN FISHES AND ITS LOSS IN AN - OMICS ERA ....................................................................................................................... 8 2.1 Abstract ..................................................................................................................... 8 2.2 Introduction ............................................................................................................... 8 2.3 Diadromy in fishes – what is known? ..................................................................... 10 2.3.1 Classification .................................................................................................... 13 2.3.2 Phylogeny and biogeography ........................................................................... 14 2.3.3 Hypotheses on the origin .................................................................................. 17 2.3.4 Loss of diadromy .............................................................................................. 19 2.4 -Omics studies in diadromous fishes – what current research tells us? .................. 22 2.4.1 Life history ....................................................................................................... 30 2.4.2 Facultative behavior ......................................................................................... 31 2.4.3 Molecular bases ................................................................................................ 33 2..4.4 Origin and ancestry .......................................................................................... 35 2.5 Future directions of diadromy in an -omics era – what we can learn?.................... 38 2.6 Concluding remarks ................................................................................................ 39 2.7 Acknowledgments ................................................................................................... 39 2.8 Author contributions ............................................................................................... 39 2.9 Supplementary information ..................................................................................... 40 CHAPTER 3. THE EFFECTS OF DIADROMY AND ITS LOSS ON GENOMIC DIVERGENCE: THE CASE OF AMPHIDROMOUS GALAXIAS MACULATUS POPULATIONS ............................................................................................................... 42 3.1 Abstract ................................................................................................................... 42 3.2 Introduction ............................................................................................................. 43 iii 3.3 Material and Methods.............................................................................................. 45 3.3.1 Study area and sample collection ..................................................................... 45 3.3.2 DNA extraction and RAD-seq pilot ................................................................. 48 3.3.3 Bait design and RADcap .................................................................................. 49 3.3.4 Data analyses .................................................................................................... 49 3.4 Results ..................................................................................................................... 51 3.4.1 Neutral loci analyses ......................................................................................... 53 3.4.2 Outlier loci analyses ......................................................................................... 58 3.5 Discussion ............................................................................................................... 60 3.5.1 Diadromous populations ................................................................................... 60 3.5.2 Resident populations......................................................................................... 62 3.5.3 Diadromous vs Resident ................................................................................... 63 3.5.4 Methodological considerations, conservation implications, and future directions ................................................................................................................... 65 3.6 Acknowledgements ................................................................................................. 66 3.7 Author contributions ............................................................................................... 67 3.8 Supplementary information ..................................................................................... 67 CHAPTER 4. GENOMIC BASIS OF THE LOSS OF DIADROMY IN GALAXIAS MACULATUS: INSIGHTS FROM RECIPROCAL TRANSPLANT EXPERIMENTS 77 4.1 Abstract ................................................................................................................... 77 4.2 Introduction ............................................................................................................. 78 4.3 Materials and methods ............................................................................................ 80 4.3.1 Study area ......................................................................................................... 80 4.3.2 Reciprocal transplant ........................................................................................ 81 4.3.3 Genomic data .................................................................................................... 83 4.3.4 Data analysis ..................................................................................................... 84 4.4 Results ..................................................................................................................... 85 4.4.1 Reciprocal transplant ........................................................................................ 85 4.4.2 Genomic analyses ............................................................................................. 86 4.5 Discussion ............................................................................................................... 93 4.5.1 The genetic basis of salinity tolerance .............................................................. 95 4.5.2 The genetic basis of local adaptation ................................................................ 97 4.5.3 Experimental considerations and future directions .......................................... 98 iv 4.6 Acknowledgements ............................................................................................... 100 4.7 Author contributions ............................................................................................. 100 4.8 Supporting information ......................................................................................... 100 CHAPTER 5. GENE EXPRESSION VARIATION ASSOCIATED WITH THE LOSS OF DIADROMY AND UPPER SALINITY TOLERANCE IN GALAXIAS MACULATUS ......................................................................................................................................... 112 5.1 Abstract ..................................................................................................................... 112 5.2 Introduction ........................................................................................................... 113 5.3 Materials and Methods .......................................................................................... 116 5.3.1 Fish collection................................................................................................. 116 5.3.2 Lab acclimation (0 ppt) and salt water (23-25) ppt transfer experiment ........ 117 5.3.3 Sampling and data collection .........................................................................