W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2008 A Molecular Analysis of Atlantic Menhaden (Brevoortia tyrannus) Stock Structure Abigail J. Lynch College of William and Mary - Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Fresh Water Studies Commons, Molecular Biology Commons, and the Oceanography Commons Recommended Citation Lynch, Abigail J., "A Molecular Analysis of Atlantic Menhaden (Brevoortia tyrannus) Stock Structure" (2008). Dissertations, Theses, and Masters Projects. Paper 1539617866. https://dx.doi.org/doi:10.25773/v5-rw45-j035 This Thesis is brought to you for free and open access by the Theses, Dissertations, & Master Projects at W&M ScholarWorks. It has been accepted for inclusion in Dissertations, Theses, and Masters Projects by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. A Molecular Analysis of Atlantic Menhaden (Brevoortia tyrannus) Stock Structure A Thesis Presented to The Faculty of the School of Marine Science The College of William and Mary in Virginia In Partial Fulfillment Of the Requirements for the Degree of Master of Science by Abigail J. Lynch 2008 APPROVAL SHEET This thesis is submitted in partial fulfillment of the requirements for the degree of Master of Science i igail J. Lynch Approved by the Committee, July 21, 2008 John Ei Graves, Ph.D. Committee Chairman/Advisor cD owell, Ph.IJNJan R. cDowell, Ph.IJNJan Robert J. Latour, Ph.D. M. Brubaker, Ph.D. TABLE OF CONTENTS Page ACKNOWLEDGMENTS..................................................................................................................v LIST OF TABLES.............................................................................................................................. vi LIST OF FIGURES..........................................................................................................................viii ABSTRACT........................................................................................................................................... 2 INTRODUCTION................................................................................................................................3 “ The Most Important Fish in the Sea ” .............................................................................. 6 Atlantic Menhaden Stock Structure Analyses .................................................................. 8 Clupeiform Genetic Stock Structure Analyses ............................................................... 10 PROJECT OBJECTIVES.................................................................................................................15 MATERIALS AND METHODS.................................................................................................... 18 Sample Collection .................................................................................................................19 Molecular Markers ...............................................................................................................19 Extraction and Amplification .............................................................................................20 Nuclear Cloning .................................................................................................................... 21 Sequence Analysis .................................................................................................................22 Microsatellite Analysis .........................................................................................................23 Descriptive Statistics ............................................................................................................ 23 Genetic Relationships ..........................................................................................................25 Population Structure ............................................................................................................ 27 RESULTS.............................................................................................................................................29 Evaluation of Mitochondrial Gene Region Variability ................................................30 Cytochrome c Oxidase Subunit 1 ...................................................................................... 31 Internal Transcribed Spacer 1 ...........................................................................................34 Microsatellites ........................................................................................................................34 Analysis of Molecular Variance ....................................................................................... 35 DISCUSSION......................................................................................................................................38 Molecular Markers ...............................................................................................................39 Species Identification ...........................................................................................................40 Phyl oge ography .................................................................................................................... 47 Population Structure ............................................................................................................49 Implications for Management ............................................................................................53 LITERATURE CITED..................................................................................................................... 97 APPENDICES.................................................................................................................................. I l l V ITA ....................................................................................................................................................120 ACKNOWLEDGMENTS I am sincerely grateful to my advisor, Dr. John Graves, and committee members, Drs. Jan McDowell, Robert Latour, and John Brubaker for their guidance and support. In particular, thanks to Dr. Graves: I appreciate his patience with my struggles and his drive to educate me in a scholarly manner which will motivate me throughout my career and life; to Dr. McDowell: her readiness to share her vast knowledge and aid others is both selfless and inspirational; to Dr. Latour: for the intellectual seed that came to this fruition and for an analytical exposure to quantitative fisheries which I could entirely be lacking with this type of study; and to Dr. Brubaker: for taking on yet another genetics project with an inspiring willingness to appreciate disciplines beyond his own. This project was accomplished with help from many colleagues, friends, and family. For specimen collection, I extend my gratitude to Gary Nelson, Heather Corbett, Patrick Lynch, Troy Tuckey, John Archambault, William Dailey, and Joel Anderson. Anderson and Brian Tarbox also gave me advice on directions in menhaden genetics and primers. Many thanks to the grounding (in)sanity of Graves Lab family: Ana Verissimo, Dan Dutton, Dave Portnoy, Emily Chandler, Kirsten Brendtro, Laurie Sorenson, and Melissa Paine. With you all, the countless hours in the lab and office were bearable, informative, and entertaining. I am thoroughly indebted to the lunch bunch, my housemates, classmates, and friends at VIMS: Andre Buchheister, Candi Spier, Chris Magel, Josh Bearman, Justine Woodward, Karen Capossela, Kathleen McNamee, Kelli Milleville, Laura Palomo, Maggie Fagan, Patrick Lynch, and Sally Upton, among many others. VIMS has been a truly irreplaceable experience because of you, your empathy, and your insightful reparte. I am also grateful to Jarrad Kosa and the U.S. Fish and Wildlife Service’s Branch of Fish and Wildlife Management Assistance for their understanding and accommodation of my degree requirements during my fellowship year. Many thanks to all my family and friends, especially my parents, Dennis and Debbie Lynch, my sisters, Nora and Annie Lynch, my grandmothers, Jean Hall and Alfina Lynch, and my aunt and uncle, Grace and Ed Simpson, for their unending encouragement and support of my educational pursuits. Funding for this project was provided by the Virginia Saltwater Recreational Fishing Development Fund (award date: 01 Jan 2007 - 31 Dec 2007). LIST OF TABLES Table Page 1. Microsatellite loci tested in the present study for amplification in Brevoortia specimens .................................................................................. 57 2. Sequence statistics of Brevoortia specimens based on an initial survey of mitochondrial control region, cytochorme c oxidase subunit I (COI), and internal transcribed spacer 1 (ITS-1) sequence data .......................................................... 62 3. Sequence statistics of Brevoortia specimens based on cytochorme c oxidase subunit I (COI) sequence data by region and overall samples ..........................................................................................................63 4. Contingency table testing the independence of geographic representation of two cytochorme c oxidase subunit I (COI) clades of large-scaled Brevoortia specimens ............................................................................... 64 5. Population statistics of Brevoortia specimens