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And Brown Trout (Salmo Trutta L.) UCC Library and UCC researchers have made this item openly available. Please let us know how this has helped you. Thanks! Title The study of molecular variation in Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.) Author(s) O'Toole, Ciar Publication date 2014 Original citation O'Toole, Ciar. 2014. The study of molecular variation in Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.). PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2014, Ciar O'Toole. http://creativecommons.org/licenses/by-nc-nd/3.0/ Item downloaded http://hdl.handle.net/10468/1932 from Downloaded on 2021-09-23T17:31:56Z The study of molecular variation in Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.) Ciar O’Toole, B.Sc. (Hons.), M.Sc. A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy. Research supervisors: Professor Tom Cross, Dr. Philip McGinnity Head of School: Professor John O’Halloran School of Biological, Earth and Environmental Sciences National University of Ireland, Cork January 2014 Table of Contents Declaration ................................................................................................................... 1 Acknowledgements ...................................................................................................... 2 General Abstract........................................................................................................... 4 Chapter 1: General Introduction .............................................................................. 5 1.1 Salmonid Biology and Life History ....................................................................... 5 1.2 Molecular Techniques and Evolutionary Implications .......................................... 9 1.2.1 Evolutionary Implications ................................................................................. 11 1.3 Atlantic salmon population genetics .................................................................... 13 1.4 Brown trout population genetics .......................................................................... 15 1.5 Invasive Species ................................................................................................... 19 1.6 Management and Conservation ............................................................................ 25 1.7 Background to Project .......................................................................................... 26 1.8 Main Hypotheses of the Thesis ............................................................................ 26 1.9 References ............................................................................................................ 28 Chapter 2: Investigating local adaptation in Salmo salar, L.: assessing the relative fitness of native and non-native salmon in a common garden experiment in the wild. .......................................................................................... 36 Abstract ...................................................................................................................... 37 2.1 Introduction .......................................................................................................... 38 2.1.1 Main Hypothesis: .......................................................................................... 41 2.2 Methods ................................................................................................................ 42 2.2.1 Experimental populations and their source locations.................................... 42 2.2.2 Hatchery methods.......................................................................................... 45 2.2.3 Freshwater Phase ........................................................................................... 48 2.2.4 Marine Phase ................................................................................................. 51 2.2.5 Molecular analysis ........................................................................................ 52 2.2.6 Data Analysis ................................................................................................ 54 2.3 Results .................................................................................................................. 57 2.3.1 Genetic Variation .......................................................................................... 57 2.3.2 Fertilization to eyed egg stage and hatchery stage ........................................ 57 2.3.3 Juveniles in freshwater .................................................................................. 61 2.3.4 Marine Survival ............................................................................................. 70 2.3.5 Overall Lifetime Success .............................................................................. 74 2.4 Discussion ............................................................................................................ 76 2.5 References ............................................................................................................ 83 Appendix I, Chapter 2: Broodstock details ................................................................ 88 Appendix II, Chapter 2: Stripping details .................................................................. 90 Appendix III, Chapter 2: Survival of subsampled eyed eggs retained in hatchery. ... 94 Appendix IV, Chapter 2: PCR recipes ....................................................................... 96 Appendix V, Chapter 2: Summary statistics for population genetics parameters...... 98 Appendix VI, Chapter 2: Means and SE for Length, and weight for all groups ........ 99 Appendix VII, Chapter 2: Electrofishing details...................................................... 100 Appendix VIII, Chapter 2: Survival model .............................................................. 101 Chapter 3: The genetic anatomy of an invasion: a case study using Salmo trutta L. from Newfoundland, Canada ........................................................................... 103 Abstract .................................................................................................................... 104 3.1 Introduction ........................................................................................................ 105 3.1.1 Recorded history of the introduction of brown trout to Newfoundland...... 106 3.1.2 Main Hypotheses of this Chapter ................................................................ 109 3.2 Materials and Methods ....................................................................................... 110 3.2.1 Site description: The Avalon Peninsula, Newfoundland, Canada .............. 110 3.2.2 Sample collection ........................................................................................ 111 3.2.3 Molecular analysis ...................................................................................... 114 3.2.4 Statistical analysis ....................................................................................... 116 3.3 Results ................................................................................................................ 120 3.3.1 Intra sample variation .................................................................................. 120 3.3.2 Inter sample variation (temporal) ................................................................ 121 3.3.3 Inter sample variation (spatial) ................................................................... 123 3.4 Discussion .......................................................................................................... 135 3.5 References .......................................................................................................... 140 Appendix I, Chapter 3: Celtic Sea Trout Project Multiplex Panels ......................... 144 Appendix II, Chapter 3: Summary statistics for population genetics parameters. ... 146 Appendix III, Chapter 3: Allele frequencies and allelic compositions for all loci .. 149 Appendix IV, Chapter 3: Exact tests between temporal samples at each site.......... 161 Chapter 4: Population genetics of Salmo trutta L., from the Currane catchment, SW Ireland and individual assignment of rod-caught specimen sea trout from Lough Currane ....................................................................................................... 162 Abstract .................................................................................................................... 163 4.1 Introduction ........................................................................................................ 164 4.1.1 Main Hypotheses of the Chapter- ............................................................... 168 4.2 Materials and Methods ....................................................................................... 169 4.2.1 Site Description ........................................................................................... 169 4.2.2 Sample collection ........................................................................................ 171 4.2.3 Molecular analysis ...................................................................................... 173 4.2.4 Statistical analysis ....................................................................................... 174 4.3 Results ................................................................................................................ 175 4.3.1
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