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Population Structure of River Herring (Alewife, Alosa Pseudoharengus, and Blueback Herring, Alosa Aestivalis) Examined Using Neutral Genetic Markers

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Population Structure of River Herring (Alewife, Alosa Pseudoharengus, and Blueback Herring, Alosa Aestivalis) Examined Using Neutral Genetic Markers Population Structure of River Herring (Alewife, Alosa pseudoharengus, and Blueback Herring, Alosa aestivalis) Examined using Neutral Genetic Markers by Meghan C. McBride Submitted in partial fulfilment of the requirements for the degree of Master of Science at Dalhousie University Halifax, Nova Scotia March 2013 © Copyright by Meghan C. McBride, 2013 DALHOUSIE UNIVERSITY DEPARTMENT OF BIOLOGY The undersigned hereby certify that they have read and recommend to the Faculty of Graduate Studies for acceptance a thesis entitled “Population Structure of River Herring (Alewife, Alosa pseudoharengus, and Blueback Herring, Alosa aestivalis) Examined using Neutral Genetic Markers” by Meghan C. McBride in partial fulfilment of the requirements for the degree of Master of Science. Dated: March 21, 2013 Supervisor: _________________________________ Readers: _________________________________ _________________________________ _________________________________ ii DALHOUSIE UNIVERSITY DATE: March 21, 2013 AUTHOR: Meghan C. McBride TITLE: Population Structure of River Herring (Alewife, Alosa pseudoharengus, and Blueback Herring, Alosa aestivalis) Examined using Neutral Genetic Markers DEPARTMENT OR SCHOOL: Department of Biology DEGREE: MSc CONVOCATION: May YEAR: 2013 Permission is herewith granted to Dalhousie University to circulate and to have copied for non-commercial purposes, at its discretion, the above title upon the request of individuals or institutions. I understand that my thesis will be electronically available to the public. The author reserves other publication rights, and neither the thesis nor extensive extracts from it may be printed or otherwise reproduced without the author’s written permission. The author attests that permission has been obtained for the use of any copyrighted material appearing in the thesis (other than the brief excerpts requiring only proper acknowledgement in scholarly writing), and that all such use is clearly acknowledged. _______________________________ Signature of Author iii Table of Contents List of Tables ................................................................................................................... vii List of Figures ................................................................................................................... ix Abstract ............................................................................................................................ xii List of Abbreviations and Symbols Used ..................................................................... xiii Acknowledgements ........................................................................................................ xiv Chapter 1: Introduction ................................................................................................... 1 1.1 Population Structure ...................................................................................... 1 1.2 River Herring .................................................................................................. 2 1.3 Thesis Overview .............................................................................................. 4 Chapter 2: Population Genetics of Alewife (Alosa pseudoharengus) and Blueback Herring (Alosa aestivalis) Examined using Neutral Genetic Markers ........ 6 2.1 Introduction ..................................................................................................... 6 2.2 Material and Methods .................................................................................. 10 2.2.1 Sample Collection .............................................................................10 2.2.2 Laboratory Protocol .........................................................................10 2.2.3 Statistical Analysis ............................................................................14 2.3 Results ............................................................................................................ 20 2.3.1 Population Genetic Statistics ............................................................20 2.3.2 Relationship among Populations ......................................................23 2.3.3 Population Structure .........................................................................23 2.3.4 Isolation by Distance ........................................................................29 2.3.5 Barrier Analysis ................................................................................30 2.3.6 Bottleneck Analysis ...........................................................................33 2.3.7 Effective Population Size ..................................................................33 2.4 Discussion....................................................................................................... 39 2.4.1 Spatial Patterns of Population Structure and Genetic Differentiation ............................................................................................40 2.4.2 Bottleneck and Effective Population Size .........................................43 2.4.3 Blueback Herring ..............................................................................44 iv Chapter 3: The Effects of Stocking on the Genetic Integrity of Alewife (Alosa pseudoharengus) Population Structure in Maine ......................................................... 45 3.1 Introduction ................................................................................................... 45 3.2 Material and Methods .................................................................................. 48 3.2.1 Sample Collection .............................................................................48 3.2.2 Laboratory Protocol .........................................................................48 3.2.3 Statistical Analysis ............................................................................48 3.3 Results ............................................................................................................ 57 3.3.1 Population Genetic Statistics ............................................................57 3.3.2 Relationships among Collection Sites and Temporal Replicates .....59 3.3.3 Isolation by Distance ........................................................................63 3.3.4 Migration between Populations ........................................................63 3.3.5 Bottleneck Analysis ...........................................................................69 3.3.6 Effective Population Size ..................................................................69 3.4 Discussion....................................................................................................... 73 3.4.1 Structure and Genetic Stability of Populations ................................73 3.4.2 Isolation by Distance ........................................................................74 3.4.3 Bottleneck and Effective Population Size .........................................76 3.4.4 Concluding Remarks .........................................................................77 Chapter 4: Conclusion .................................................................................................... 78 References ........................................................................................................................ 80 Appendix 1: Genetic diversity statistics per locus across populations include number of alleles (A) and range in allele size (in parentheses). Statistics per locus and location include the number of individuals (N), number of alleles (Na), observed (Ho) and expected (He) heterozygosity, inbreeding coefficient (FIS), probability of departures from HWE (P-val) and allelic richness (Ae). Bolded values indicate significant departures from HWE after sequential Bonferroni correction and ML indicates loci that are monomorphic in specific populations. Full names are given in Table 2.1. ....................................................... 90 Appendix 2: Matrix of pairwise FST estimates (θ; Weir and Cockerham 1984; below diagonal) and associated P-values (above diagonal) for both species, Alewife (within the vertical and horizontal dotted line) and Blueback Herring v (outside the vertical and horizontal dotted line). Bolded FST values indicate non-significant p-values. Full names are given in Table 2.1. ................................. 110 Appendix 3: Genetic diversity statistics per locus across collections, including number of alleles (A) and range in allele size (in parentheses). Statistics per locus and location include the number of individuals (N), number of alleles (Na), observed (Ho) and expected (He) heterozygosity, inbreeding coefficient (FIS), probability of departures from Hardy-Weinberg Equilibrium (P-val) and allelic richness (Ae). Bolded values indicate significant departures from HWE after sequential Bonferroni correction and ML indicates loci that are monomorphic in specific populations. Full names are given in Table 3.1. ............ 116 Appendix 4: Genic differentiation for Maine collections where the bolded values indicate significant p-values after sequential Bonferroni correction. Full names are given in Table 3.1. ............................................................................................ 128 Appendix 5: Pairwise FST (below diagonal) and their associated p-values (above diagonal) for Maine collections. The highly significant (p < 0.001) global FST was 0.012. The bolded values indicate significant FST values after sequential Bonferroni
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