A Molecular Study of the Mitochondrial Genome and Invasions of the Veined Rapa Whelk, Rapana Venosa
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W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2007 A Molecular Study of the Mitochondrial Genome and Invasions of the Veined Rapa Whelk, Rapana venosa Emily A. Chandler College of William and Mary - Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Molecular Biology Commons Recommended Citation Chandler, Emily A., "A Molecular Study of the Mitochondrial Genome and Invasions of the Veined Rapa Whelk, Rapana venosa" (2007). Dissertations, Theses, and Masters Projects. Paper 1539617856. https://dx.doi.org/doi:10.25773/v5-9eph-4w97 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 STUDY OF THE MITOCHONDRIAL GENOME AND INVASIONS OF THE VEINED RAPA WHELK, RAP ANA VENOSA 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 Emily A. Chandler 2007 APPROVAL SHEET This thesis is submitted in partial fulfillment of the requirements for the degree of Master of Science Emily A. Chandler Approved, April 2007 £ in E. Graves, Ph.D. ^Co-Committee Chair/Advisor Roger L.Mann, Ph.D. Co-Committee Chair/Ad visor n R. McDowell, Ph.D. 'fiA/Lf/l Deborah A. Bronk, Ph.D Robert B. Whitlatch, Ph.D. University of Connecticut Groton, CT TABLE OF CONTENTS Page ACKNOWLEDGMENTS......................................................................................................... v LIST OF TABLES........................................................................................................................vi LIST OF FIGURES.................................................. ;................................................................ vii LIST OF APPENDICES...........................................................................................................viii ABSTRACT........................................................................................................... ix INTRODUCTION......................................................................................................................... 2 CHAPTER I: Mitochondrial DNA sequence of the rapa welk {Rapana venosa) and the genetic variability of mitochondrial coding regions in the neogastropods............................................................................................... 10 INTRODUCTION..........................................................................................................11 MATERIALS AND METHODS..................................................................................14 RESULTS AND DISCUSSION...................................................................................17 Rapana venosa Mitochondrial Amplification and Gene Order Determination....................................................................................... 17 Nucleotide Variability Within Mitochondrial Gene Regions of the Neogastropods.......................................................................................22 CHAPTER II: Populations o f genetic monomorphism: A study of Rapa whelk {Rapana venosa) invasions.............................................................................. 31 INTRODUCTION..........................................................................................................32 MATERIALS AND METHODS................................................................................. 38 RESULTS........................................................................................................................ 41 DISCUSSION................................................................................................................. 44 CONCLUSION................................................................................................... 65 APPENDICES..............................................................................................................................71 LITERATURE CITED............................................................................................................... 81 VITA.............................................................................................................................................. 92 iv ACKNOWLEDGMENTS Thank you to everyone who helped make my thesis research a success. My co advisors Dr. John Graves and Dr. Roger Mann provided invaluable advice, direction, and financial support. Dr. Jan McDowell was instrumental in helping me develop my project and overcome the difficulties I encountered in the lab work. Dr. Deborah Bronk and Dr. Robert Whitlatch acted as great additions to my committee. Many thanks to the researchers who collectedRapana venosa samples for me. Dr. Huayong Que and Dr. Kimberly Reece collected samples from China. Japanese samples were sent to me by Dr. Taeko Kimura. Dr. Anna Occhipinti Ambriogi and Dr. Dario Savini graciously shared samples from Italy. France samples were sent to me by Dr. Edouard Bedier and Dr. Dennis Nieweg and Dr. Robert Vink provided samples from The Netherlands. I would also like to give a special thank you to Dr. Juliana Harding who helped me obtain samples from Chesapeake Bay, as well as shared with me her research on Rapana venosa. My research would not have been a success without the funding of the SMS graduate fellowship and support provided by the VIMS Annual Fund Committee. Thank you to all the members of Fisheries Genetics Laboratory and other friends at VIMS who entertained me along the way. Finally, I would like to thank my family and my fiance Andy for their never ending support and encouragement. v LIST OF TABLES Table Page 1. List of primers used in PCR reactions................................................................................ 24 2. List of annealing temperatures used with each primer pair.............................................26 3. Annotated Rapana venosa mitochondrial genome........................................................... 27 4. Comparison of levels of genetic variation within each mitochondrial gene region among four neogastropod species....................................................................................... 29 5. List of mitochondrial gene regions by increasing genetic variability as seen in neogastropods and mammals................................................................. 30 6. Information on Rapana venosa samples .......................................................................57 7. Population genetics statistics for eachRapana venosa collection calculated from the combined COI/ND2 sequence data............................................................... 59 8. AMOVA results of <D comparison between native collections (LB, YAN, QD, XS, J, KC, KI, KT) and introduced collections (T, A, FN, CB).................................................62 9. Ost Values for Pairwise Comparisons................................................................................. 63 LIST OF FIGURES Figure Page 1. Illustration of circular Rapana venosa mitochondrial genome........................................28 2. Map of current locations ofRapana venosa populations..................................................53 3. Locations ofRapana venosa samples taken within its native range...............................54 4. Locations ofRapana venosa samples taken from introduced populations in the Black Sea, the Adriatic Sea, Quiberon Bay, France, and off the coast of the Netherlands..............................................................................................................................55 5. Locations ofRapana venosa samples taken within Chesapeake Bay............................56 6. Minimum spanning network o f combined COI and ND2 haplotypes.......................... 60 7. Generalized diagram of prevailing currents in the native range ofRapana venosa.. .64 LIST OF APPENDICES Appendix Page 1. The nucleotide sequence of the mitochondrial genome ofRapana venosa....................72 2. A list of the variable sites present in each combined COI/ND2 haplotype.................... 77 viii ABSTRACT Rapana venosa is a predatory marine gastropod native to the coastal waters of China, Korea, and Japan. Since the 1940s,R. venosa has been transported around the globe and introduced populations now exist in the Black Sea, the Mediterranean Sea, the Adriatic and Aegean seas, off the coasts of France and The Netherlands, in Chesapeake Bay, Virginia, U.S.A, and in the Rio de la Plata between Uruguay and Argentina. Identifying the source population(s) of invasions has been recognized as an important step for understanding and potentially controlling the spread of invasive species. Recent studies of marine invasions have found that mitochondrial sequence data can be used to assess the genetic composition of native and introduced populations, allowing researchers to trace invasion pathways and determine source populations. However, amplifying regions of the mitochondrial genome in mollluscs is not always straightforward due to the high levels of gene rearrangement observed within the phylum. Additionally, choosing an appropriately variable mitochondrial gene region for intraspecific studies is difficult in gastropods