W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2012 Patterns of Population Structure and Historical Dispersal in Squaloid Sharks: A Species-Level Approach using Molecular Markers Ana Christina Pimenta Verissimo 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, Genetics Commons, Oceanography Commons, and the Zoology Commons Recommended Citation Verissimo, Ana Christina Pimenta, "Patterns of Population Structure and Historical Dispersal in Squaloid Sharks: A Species-Level Approach using Molecular Markers" (2012). Dissertations, Theses, and Masters Projects. Paper 1539616812. https://dx.doi.org/doi:10.25773/v5-z41e-2z41 This Dissertation 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]. Patterns of Population Structure and Historical Dispersal in Squaloid Sharks: a Species­ Level Approach Using Molecular Markers A Dissertation 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 Doctor of Philosophy by Ana Cristina Pimenta V erissimo 2011 APPROVAL SHEET This dissertation is submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Ana V erissimo Approved by the Committee June 20, 2011 t-~ Kimberly Reece, Ph.D. Gui M. Menez s, Ph.D. University of the Azores Horta, Azores - Portugal ii TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................................. v LIST OF TABLES ......................................................................................................................... vii LIST OF FIGURES ...................................................................................................................... viii ABSTRACT .................................................................................................................................... ix AUTHOR'S NOTE·························································································································· X INTRODUCTION ........................................................................................................................... 2 References .................................................................................................................................. 17 CHAPTER I Isolation and characterization of nuclear microsatellite loci in three squaloid sharks Squalus acanthias, Centroscymnus coelolepis and Centrophorus squamosus .................................... 25 Abstract ............................................................................................................................. 26 Introduction, Methods, Results and Discussion ................................................................ 27 References ......................................................................................................................... 32 CHAPTER2 Global population structure of the spiny dogfish Squalus acanthias, a temperate shark with an antitropical distribution .......................................................................................................... 36 Abstract ............................................................................................................................. 37 Introduction ....................................................................................................................... 3 8 Materials and Methods ...................................................................................................... 40 Results ............................................................................................................................... 45 Discussion ......................................................................................................................... 49 References ......................................................................................................................... 56 CHAPTER3 Population structure of a deep-water squaloid shark, the Portuguese dogfish ( Centroscymnus coelolepis) .............................................................................................................................. 71 iii Abstract ............................................................................................................................. 72 Introduction ....................................................................................................................... 73 Materials and Methods ...................................................................................................... 75 Results ............................................................................................................................... 79 Discussion ......................................................................................................................... 82 References ......................................................................................................................... 88 CHAPTER4 Population structure and genetic connectivity in the leafscale gulper Centrophorus squamosus ........................................................................................................................................ 103 Abstract ........................................................................................................................... 104 Introduction ..................................................................................................................... 105 Materials and Methods .................................................................................................... 108 Results ............................................................................................................................. 114 Discussion ....................................................................................................................... 119 References ....................................................................................................................... 126 CONCLUSIONS ......................................................................................................................... 141 References ................................................................................................................................ 150 VITA ............................................................................................................................................ 159 iv ACKNOWLEDGEMENTS To Dr. John Graves, my supervisor, for accepting and welcoming me into his lab, and for supporting my research plans and directing me into the "safest" and most reasonable path of research during these last years. Thank you for putting up with my persistence (some might call it stubbornness ... ), for always being available for discussing ideas and strategies, and for helping me grow as a scientist. To Dr. Jan McDowell, my friend and mentor for all things genetic and otherwise, for teaching and challenging me throughout the graduate program, for her patience and availability to help clear the fog that so often closed down on me and made me knock on her door for guidance. Thank you for all your advice, suggestions, comments, ear-pulling and support. I could not have made half so much or half so well without you. To my other committee members, Dr. Jack Musick, Dr. Kim Reece, and Dr. Gui Menezes, for their precious time and insightful comments and discussions. And to all the amazing people that spend time and energy collecting samples for my project and/or whom contributed with data and comments/criticisms to my work: Graham Johnston, Maurice Clarke, Chip Cotton, Lourdes Fernandez, Pedro Pascual-Alay6n, Rob Leslie, Peter Chase, Stacey Rowe, Jim Ellis, Darren Stevens, Richard O'Driscoll, Claire Healey, Dave Ebert, Jun Yamamoto, Ana Massa, Nico Straube, Francisco Concha, Ken Neill, Jim Franks, Gui Menezes, Joaquim Leopolda, and Joaquim P6lvora. You made this research project happen. To all my current and former lab mates, Dave Portnoy, Emily Chandler, Abby Lynch, Laurie Sorenson, Dan Dutton, Sharon Furiness, Cati Wor, Emily Loose, Ben Marcek, and Kristy Hill, for their friendliness, cheerfulness and camaraderie inside and outside the lab. It's been a pleasure working with you; you've made my workload lighter and easier. To my housemates extraordinaire, Abby Lynch and Laura Palomo, for their friendship, patience and good humor during the years we lived together. I was so very fortunate to find you two girls! You've made me a better person, helped me keep my mental sanity and never let me feel lonely. To my good friends, Samantha Sifleet, Kelli Milleville, Matt Wright, Cati Wor, Dares Cruz, Nuno Prista, Nalani Schnell, Marc, Julia and Falke Borg, Kim Bernard, Xiaodong Wang, Yongjin Xao, Yan Wang, Ines Castej6-Silvo, Althea Moore, Glaucia Fragoso, Liza Hernandez, Amy Then, Carolina Funkey, Rachael Blake, Casey Dillman, Corinne Audermad, Ryan Carnegie, Debra Parthree, Dave Gauthier, Jess Moss, Hamish Small, Barry Campbell, Andre Buchheister, Pat Lynch, Chris Magel, and the list