ECOLOGICAL SPECIATION OF A LANDLOCKED POPULATION OF RAINBOW SMELT (Osmerus mordax) IN LOCHABER LAKE, NOVA SCOTIA by Julie Rivard Submitted in partial fulfilment of the requirements for the degree of Master of Science at Dalhousie University Halifax, Nova Scotia June 2016 © Copyright by Julie Rivard, 2016 DEDICATION PAGE For my parents. ii TABLE OF CONTENTS LIST OF TABLES ................................................................................................................ v LIST OF FIGURES ............................................................................................................. vi ABSTRACT ........................................................................................................................ ix LIST OF ABBREVIATIONS USED .................................................................................. xi ACKNOWLEDGEMENTS ................................................................................................. xi CHAPTER 1 INTRODUCTION ............................................................................. 1 1.1 The study of adaptation and ecological speciation .................................................................................................. 1 1.2 Study Species........................................................................................................................................................... 6 1.3 Thesis Objectives ..................................................................................................................................................... 8 CHAPTER 2 Genetic differentiation of the small and large Rainbow smelt (Osmerus mordax) in Lochaber Lake, Nova Scotia and its stability over time .................. 10 2.1 Intoduction ............................................................................................................................................................. 10 2.1.1 Chapter Objectives ........................................................................................................................... 15 2.2 Materials and Methods .......................................................................................................................................... 15 2.2.1 Study Area ....................................................................................................................................... 15 2.2.2 Field Methods .................................................................................................................................. 16 2.2.3 DNA isolation and data collection ................................................................................................... 16 2.2.4 Data Analyses .................................................................................................................................. 19 2.3 Results 22 2.3.1 Data quality ...................................................................................................................................... 22 2.3.2 Genetic Analysis .............................................................................................................................. 22 2.3.3 Gene flow between small and large smelt morphs ........................................................................... 31 2.4. Discussion ............................................................................................................................................................ 31 2.5 Conclusion ............................................................................................................................................................. 40 CHAPTER 3 Morph and hybrid identity of larvae in a landlocked sympatric pair of Rainbow Smelt (Osmerus mordax) in Lochaber Lake, Nova Scotia ............................. 42 3.1 Introduction ........................................................................................................................................................... 42 3.1.1 Chapter Objectives ........................................................................................................................... 45 3.2 Materials and Methods .......................................................................................................................................... 45 iii 3.2.1 Study Area ....................................................................................................................................... 45 3.2.2 Field Methods .................................................................................................................................. 46 3.2.3 DNA isolation and data collection ................................................................................................... 46 3.2.4 Data Analyses .................................................................................................................................. 49 3.2.5 Individual assignment tests .............................................................................................................. 51 3.2.6 Bayesian tests for hybridization ....................................................................................................... 51 3.3 Results 52 3.3.1 Data quality ...................................................................................................................................... 52 3.3.2 Genetic Diversity ............................................................................................................................. 52 3.3.3 Gene flow between small and large smelt morphs ........................................................................... 59 3.3.4 Individual Assignment Test ............................................................................................................. 59 3.3.5 Hybridization analysis...................................................................................................................... 60 3.4 Discussion ............................................................................................................................................................. 61 3.5 Conclusion ............................................................................................................................................................. 70 CHAPTER 4 Thesis Conclusion ............................................................................ 71 APPENDICES ............................................................................................................................................................. 72 BIBLIOGRAPHY ....................................................................................................................................................... 86 iv LIST OF TABLES Table 2.1. Pairwise FST values and p-values for all samples of rainbow smelt from Lochaber Lake calculated using a permutation test implemented in MSA. ............................................... 24 Table 2.2. Estimated rate of gene flow between the small and large morph, obtained using BayesAss. Values that differ significantly from zero, based on 95% confidence intervals, are in bold and underlined. Values marked with N/A are the same as the values below them, as Omo2 was not genotyped for 2002 and 2003 samples............................................................... 33 Table 3.1. Date and number or larval smelt caught in 2010 and 2011 versus the number of larval smelt genotyped. .............................................................................................................. 48 Table 3.2. Results obtained from most of the data analyses showing the same trend between the small, large and larval smelt. ................................................................................................ 66 v LIST OF FIGURES Figure 2.3. Principle coordinate analysis for adult smelt ecotypes collected in 2002 (N=225, 191 small & 34 large morph). Results shown are a) all 7 microsatellite loci; b) 6 microsatellite loci with Omo14 removed; c) 6 microsatellite loci with Omo2 removed and d) 5 microsatellite loci with both Omo2 & Omo14 removed. All four plots show two dimensions of genetic variation; numbers in parentheses show percentage of genetic variation explained by one axis. .................................................................................................................................................... 25 Figure 2.4. Principle coordinate analysis for adult smelt ecotypes collected in 2003 (N=179, 136 small & 43 large morph). Results shown are a) all 7 microsatellite loci; b) 6 microsatellite loci with Omo14 removed; c) 6 microsatellite loci with Omo2 removed and d) 5 microsatellite loci with both Omo2 & Omo14 removed. All four plots show two dimensions of genetic variation; numbers in parentheses show percentage of genetic variation explained by one axis. .................................................................................................................................................... 26 Figure 2.5. Principle coordinate analysis for adult smelt ecotypes collected in 2004 (N=310, 190 small & 120 large morph). Results shown are a) all 7 microsatellite loci; b) 6 microsatellite loci with Omo14 removed; c) 6 microsatellite loci with Omo2 removed and d) 5 microsatellite loci with both Omo2 & Omo14 removed. All four plots show two dimensions of genetic variation; numbers in parentheses show percentage of genetic variation explained by one axis. .....................................................................................................................................