UNIVERSITY OF CALIFORNIA SANTA CRUZ CONSERVATION GENETICS OF COMMERCIALLY EXPLOITED FISHES WITH CASE STUDIES ON LEOPARD AND NASSAU GROUPER A dissertation submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in ECOLOGY AND EVOLUTIONARY BIOLOGY by Alexis Michelle Jackson March 2014 The Dissertation of Alexis Michelle Jackson is approved: ____________________________________ Professor Yvonne Sadovy de Mitcheson ____________________________________ Professor Pete Raimondi ____________________________________ Professor Don Croll ____________________________________ Assistant Professor Brice Semmens ____________________________________ Adjunct Professor Devon Pearse ____________________________________ Professor Giacomo Bernardi, Chair ____________________________________ Tyrus Miller Vice Provost and Dean of Graduate Studies Copyright ! by Alexis Michelle Jackson 2014 Contents List of Figures................................................................................................................v List of Tables ............................................................................................................... vi Abstract...................................................................................................................... viii Dedication......................................................................................................................x Acknowledgements...................................................................................................... xi Introduction..................................................................................................................1 Chapter 1 Population structure and larval retention in Nassau grouper (Epinephelus striatus), a mass-aggregating marine fish ...........................................5 1.1 Introduction.............................................................................................................6 1.2 Materials and Methods..........................................................................................10 1.2.1 Sample collection and DNA extraction .....................................................10 1.2.2 Genotyping and data analysis for mitochondrial markers .........................11 1.2.3 Genotyping and data analysis for microsatellite loci.................................12 1.2.4 Genotyping and data analysis for single nucleotide polymorphisms.........13 1.2.5 Population structure ...................................................................................14 1.3 Results...................................................................................................................16 1.3.1 Mitochondrial DNA...................................................................................16 1.3.2 Microsatellites............................................................................................17 1.3.3 Single nucleotide polymorphisms..............................................................17 1.3.4 Population structure ...................................................................................18 1.4 Discussion.............................................................................................................20 1.4.1 Timing of ocean currents with reproduction may facilitate larval retention .....................................................................................................22 1.4.2 Evidence of limited dispersal in marine species........................................25 1.5 Conclusion ............................................................................................................31 Chapter 2 Historical and ecological genetics of Leopard grouper (Mycteroperca rosacea) in the Gulf of California .............................................................................44 2.1 Introduction...........................................................................................................45 2.2 Materials and Methods..........................................................................................49 2.2.1 Sample collection and DNA extraction .....................................................49 2.2.2 Genotyping and data analysis for mitochondrial markers .........................50 2.2.3 Genotyping and data analysis for microsatellite loci.................................51 2.2.4 Divergence estimates and demographic patterns.......................................51 2.2.5 Population structure ...................................................................................53 2.2.6 Migration patterns......................................................................................54 iii 2.3 Results...................................................................................................................55 2.3.1 Genetic data: Mitochondrial markers.........................................................55 2.3.2 Genetic data: Microsatellite markers .........................................................55 2.3.3 Divergence estimates and demographic patterns.......................................56 2.3.4 Population structure ...................................................................................57 2.3.5 Migration patterns......................................................................................59 2.4 Discussion.............................................................................................................59 2.4.1 Demographic history .................................................................................59 2.4.2 Contemporary mechanisms restricting gene flow......................................60 2.4.3 Relevance for conservation and fisheries management ............................63 2.5 Conclusion ............................................................................................................66 Chapter 3 How does the magnitude of genetic differentiation impact fisheries management strategies? ............................................................................................75 3.1 Introduction...........................................................................................................76 3.2 Methods.................................................................................................................78 3.2.1 Literature review........................................................................................78 3.2.2 Inclusion and exclusion criteria .................................................................79 3.2.3 Data collection and analysis.......................................................................79 3.3 Results and Discussion .........................................................................................81 3.3.1 Study characteristics ..................................................................................81 3.3.2 Quantitative adjectives for magnitudes of genetic differentiation.............82 3.3.3 Common fisheries management recommendations ...................................84 3.3.4 Relationship between magnitude of genetic differentiation and stock management strategies...............................................................................85 3.3.5 Potential biases associated with use of FST in designating management strategies ....................................................................................................88 3.4 Conclusion ............................................................................................................89 Appendix A. Supplementary Material for Chapter 1............................................99 Appendix B. Supplementary Material for Chapter 2..........................................102 Appendix C. Supplementary Material for Chapter 3..........................................109 References.................................................................................................................121 iv List of Figures Figure 1.1. Nassau grouper sampling localities in the Caribbean Sea.........................40 Figure 1.2. Haplotype network for Nassau grouper.....................................................41 Figure 1.3. Identified barriers to larval dispersal in the Caribbean Sea.......................42 Figure 1.4. Bayesian population assignment tests for Nassau grouper........................43 Figure 2.1. M. rosacea sampling localities in the Gulf of California ..........................70 Figure 2.2. Coalescent genealogy for M. rosacea .......................................................71 Figure 2.3. Pie diagrams for M. rosacea......................................................................72 Figure 2.4. Identified barriers to larval dispersal in the Gulf of California.................73 Figure 2.5. Reconstruction of Gulf of California coastline during the last glacial maximum (LGM) ........................................................................................74 Figure 3.1. Taxonomic bias of studies.........................................................................95 Figure 3.2. Relationship between FST and quantitative adjectives for genetic differentiation .............................................................................................96 Figure 3.3. Recommended fisheries management strategies.......................................97 Figure 3.4. Relationship between stock management approach and magnitudes of genetic differentiation .....................................................................98 Figure