The Demographic History and Population Structure of Three Species of Wolffishes Across the North Atlantic Ocean by Megan R. McCusker Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Dalhousie University Halifax, Nova Scotia April 2009 © Copyright by Megan R. 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Canada DALHOUSIE UNIVERSITY To comply with the Canadian Privacy Act the National Library of Canada has requested that the following pages be removed from this copy of the thesis: Preliminary Pages Examiners Signature Page (pii) Dalhousie Library Copyright Agreement (piii) Appendices Copyright Releases (if applicable) Dedication I dedicate this thesis to my husband, Arturo Orellana, and son, Javier Orellana. Thank you for your patience and support throughout my Ph.D. IV Table of Contents List of Tables xi List of Figures xv Abstract xviii Acknowledgements xix Chapter 1: Introduction 1 Chapter 2: Mitochondrial and Microsatellite Genetic Diversity is Correlated with Abundance in Fishes 3 2.1 Abstract 3 2.2 Introduction 3 2.3 Materials & Methods 6 2.3.1 Data Collection 6 2.3.2 Analysis ,..7 2.4 Results 10 2.5 Discussion 18 Chapter 3: Phylogeography of Three North Atlantic Wolffish Species (Anarhichas spp.) with Phylogenetic Relationships within the Family Anarhichadidae ; 26 3.1 Abstract 26 3.2 Introduction 26 3.3 Materials & Methods 29 3.3.1 Phylogenetic Relationships and Speciation Timing 30 3.3.2 Intra-specific Variation 32 V 3.4 Results 34 3.4.1 Phylogenetic Relationships 34 3.4.2 Mutation Rates and Speciation Timing 36 3.4.3 Intra-specific Variation 37 3.4.4 Population Expansion and Intra-specific Divergence 38 3.5 Discussion 41 3.5.1 Origins of Family Anarhichadidae 41 3.5.2 Post-glacial Population Expansion 42 3.5.3 Mutation Rate Estimate 43 3.5.4 Glacial Refugia 45 3.5.5 Conservation Implications 46 Chapter 4: Microsatellite Markers Discriminate Three Species of North Atlantic Wolffishes (Anarhichas spp.) 57 4.1 Abstract 57 4.2 Introduction 57 4.3 Materials & Methods 59 4.3.1 Sample Collection 59 4.3.2 Genetic Analysis 59 4.3.3 Statistical Methods 62 4.4 Results 63 4.4.1 Microsatellite Characteristics 63 4.4.2 Species-Level Identification 65 4.5 Discussion 65 vi Chapter 5: Historical Influences Dominate the Population Genetic Structure of a Sedentary Marine Fish, Atlantic wolffish (Anarhichas lupus), Across the North Atlantic Ocean 69 5.1 Abstract 69 5.2 Introduction 69 5.3 Materials & Methods 72 5.3.1 Sample and Data Collection 72 5.3.2 Analytical Methods 74 53.2.1 Microsatellites 74 5.3.2.UAFLP 76 5.4 RESULTS 77 5.4.1 Microsatellite Characteristics 77 5.4.2 Population Structure and Dispersal 78 5.4.3 Effective Population Size and Historical Demography 80 5.4.4 AFLP Characteristics 82 5.5 DISCUSSION 84 5.5.1 Population Structure Across the Range of Atlantic Wolffish 84 5.5.2 The Role of Contemporary vs. Historical Factors 87 5.5.3 AFLP vs. Microsatellites 91 5.5.4 Conservation Implications 92 Chapter 6: Genetic Variation in Northern and Spotted Wolffishes (Anarhichas denticulatus and A. minor) Across the North Atlantic Ocean: Low Effective Population Sizes in Two 'Threatened' Species 101 6.1 Abstract 101 6.2 Introduction 101 Vll 6.3 Materials & Methods 104 6.3.1 Sample and Data Collection 104 6.3.2 Analytical Methods 106 6.4 Results 109 6.4.1 Microsatellite Characteristics 109 6.4.2 AFLP Characteristics 110 6.4.3 Population Structure and Dispersal Ill 6.4.3.1 Northern Wolffish Ill 6.4.3.U Spotted Wolffish 114 6.4.4 Bottlenecks and Effective Population Size 115 6.5 Discussion 118 6.5.1 Microsatellite and AFLP Comparisons 118 6.5.2 Dispersal and Life History 121 6.5.3 Effective Population Size 123 6.5.4 Conclusion 125 Chapter 7: Conclusion 132 Reference List 135 Appendix 1. List of marine fishes and citations used 182 Appendix 2. List of freshwater and diadromous fishes and citations used 186 Appendix 3. Observed and expected heterozygosity for freshwater/diadromous (above) and marine fishes (below) relative to sample sizes. Only sample sizes less than 100 are shown 190 Appendix 4. Representative graphs of the relationships between diversity and sample size in the primary dataset (all fishes). Only sample sizes less than 100 are shown 191 Vlll Appendix 5. Graphs of the highest correlations between genetic diversity and catch. Those for mtDNA data are from Tables 5 and 5b and those for microsatellite data are from Table 4 193 Appendix 6. MtDNA primers DL-F, DL-R, ND1-F, and ND1-R were used for PCR amplification. Internal primers (labeled with "Int") were used for sequencing PCR (see text) 195 Appendix 7. Amino acid variation at the following amino acid sites in the ND1 region within the family Anarhichadidae. Blanks indicate no change in amino acid from the first one listed 195 Appendix 8. Haplotypes found across the range of Atlantic wolffish. Haplotype numbers correspond with the phylogenetic tree and minimum spanning networks (Figures 4, 7) 196 Appendix 9. Haplotypes found across the range of spotted wolffish. Haplotype numbers correspond with the phylogenetic tree and minimum spanning networks (Figures 4, 7) 197 Appendix 10. Haplotypes found across the range of northern wolffish. Haplotype numbers correspond with the phylogenetic tree and minimum spanning networks (Figures 4, 7) 197 Appendix 11. Dominant current patterns in the North Atlantic Ocean (http ://www.mar-eco.no/learning-zone/ data/page/471 /currentl _LG.jpg) 198 Appendix 12. Number of alleles and expected heteroyzogisty per sample across 14 loci used for population analysis in Atlantic wolffish 199 Appendix 13. AFLP diversity data from AFLP-Surv (Lynch and Milligan method). Polymorphic loci are defined as those with allele frequencies between 5-95%. Hj is expected heterozygosity assuming Hardy-Weinberg genotypic proportions 200 Appendix 14. Characteristics of fifteen microsatellite loci in northern and spotted wolffishes 201 Appendix 15a. Northern wolffish population data from AFLP-SURV [Lynch & Milligan method]: frequency-based (upper) and Bayesian approach (lower) 202 Appendix 15b. Spotted wolffish population data from AFLP-SURV [Lynch & Milligan method]: frequency-based (upper) and Bayesian approach (lower) 202 IX Appendix 16. Chebyshev inequality based on effective densities of 10 for northern and spotted wolffishes (ind km"1). Slopes used for this analysis were based on range-wide FST for northern wolffish and with Barents Sea samples removed for spotted wolffish 203 Appendix 17. Comparative sizes of microsatellite repeat arrays among three wolffish species for loci found to be monomorphic in either spotted or northern wolffishes 203 Appendix 18. Copyright permission for Chapter 3 204 Appendix 19. Copyright permission for Chapter 4 205 X List of Tables Table 1. Correlation statistics between genetic diversity and catch statistics for the original dataset (top) and for those data with sample sizes >20 for mtDNA and >40 for microsatellites. Significant correlations (p<0.05) are highlighted in gray 12 Table 2. Correlation statistics between genetic diversity and body size for the original dataset (top) and for those data with sample sizes >20 for mtDNA and >40 for microsatellites. Significant correlations (p<0.05) are highlighted in gray 13 Table 3. Correlation statistics between mtDNA and microsatellite diversity for marine, FW-anadromous species, and for the combined data set. Significant correlations (p<0.05) are highlighted in gray 14 Table 4. The effect of number of microsatellite loci on correlations between abundance (catch, size) and genetic diversity. Results based on data with sample sizes of 40 or more are also presented. Significant correlations (p<0.05) are highlighted in gray 15 Table 5a. Results for three different classifications of mtDNA: CR, non-CR, and mixture. Significant correlations (p<0.05) are highlighted in gray 16 Table 5b. Results for three different classifications of mtDNA: CR, non-CR, and mixture.