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AN ABSTRACT OF THE DISSERTATION OF Rebecca E. B. Baldwin for the degree of Doctor of Philosophy in Fisheries Science Presented on September 21, 2010. Title: Using Parasite Community Data and Population Genetics for Assessing Pacific Sardine (Sardinops sagax) Population Structure Along the West Coast of North America Abstract approved: Kym C. Jacobson Michael A. Banks Pacific sardines (Sardinops sagax) are an economically and ecologically important forage fish which transfer energy from planktonic primary producers and secondary consumers to upper trophic predators. Previous genetics studies of Pacific sardine suggested a panmictic population with a shallow genetic structure. However, more than one subpopulation within the Central California Offshore management unit may exist based on recovering larger individuals at higher latitudes and a temporal difference in sardine spawning off Southern California and the Pacific Northwest. Potential for separate sardine subpopulations questions the long-standing paradigm of an annual migration of individuals to feeding grounds off the Pacific Northwest in the summer with migrants returning to Southern California in the fall to spawn the following spring. This study applied parasite community analyses and population genetics techniques to assess migration patterns and stock structure of Pacific sardine in the California Current from Vancouver Island, British Columbia, Canada to San Diego, California, USA. A coastwide sardine migration is supported by the geographical distribution of Myosaccium ecaude (Trematoda), but a second migration pattern was identified within the Pacific Northwest from the geographic distribution of Lecithaster gibbosus (Trematoda). Population genetics studies identified a panmictic distribution for: 1) the trematode M. ecaude using a 283bp portion of the NADH- dehydrogenase subunit 1 (ND1) mitochondrial DNA (mtDNA) gene; and 2) three species of Anisakis nematodes (A. simplex s.s., A. pegreffii, and A. simplex „C‟) using a 524bp portion of the cytochrome c oxidase 2 (cox2) mtDNA gene. These results suggest that the extensive movement of all of the potential hosts utilized by these parasites, the limited oceanographic barriers, and complexity in the California Current are not preventing the mixing of M. ecaude or Anisakis species populations. The diversity and availability of fish and cetacean species that undergo extensive migrations along the full length of the California Current system may enable large geographically distributed population sizes of these parasite species. We thus cannot confirm the existence of separate Pacific sardine subpopulations within the California Current by the occurrence of parasite communities or the population genetics analyses of M. ecaude or the three Anisakis species. ©Copyright by Rebecca E. B. Baldwin September 21, 2010 All Rights Reserved Using Parasite Community Data and Population Genetics for Assessing Pacific Sardine (Sardinops sagax) Population Structure Along the West Coast of North America by Rebecca E. B. Baldwin A DISSERTATION submitted to Oregon State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Presented September 21, 2010 Commencement June 2011 Doctor of Philosophy dissertation of Rebecca E. B. Baldwin presented on September 21, 2010. APPROVED: Co-Major Professor, representing Fisheries Science Co-Major Professor, representing Fisheries Science Head of the Department of Fisheries and Wildlife Dean of the Graduate School I understand that my dissertation will become part of the permanent collection of Oregon State University libraries. My signature below authorizes release of my dissertation to any reader upon request. Rebecca E. B. Baldwin, Author ACKNOWLEDGEMENTS My time living in Newport, Oregon and working at the Hatfield Marine Science Center is continually being filled with adventure, friendships with so many wonderful people, and learning how to be a better scientist. Many thanks are given to my co- major professors Dr. Kym Jacobson and Dr. Michael Banks. Kym: thank-you for hiring a recently-minted parasitologist from the Canadian prairies and introducing me to marine parasite ecology. You continue to kindle my passion for parasitology and your encouragement is unparalleled. Michael: thank-you for guiding me through the concepts of population genetics, and your patience with a student unfamiliar with genetics. Many thanks are given to my committee members Dr. Robert Emmett, Dr. Michael Blouin, Dr. Virginia Lesser and Dr. John Bolte for their helpful suggestions and guidance throughout my time as a Ph.D. student. Thank-you to all past and present members of the Jacobson Parasitology Lab. Mary Beth Rew, Andrew Claxton, and James Losee you have gone above and beyond to help me with my seemingly endless questions, insightful discussions on interpreting data and editing all the draft copies of chapters. Thanks to Justin Atkins and Nick Hempfer for assisting me with examining fish for parasites. Thanks also go out to the past and present members of the Banks Genetics Lab. Dave Jacobson, thanks for getting me started on proper techniques for processing DNA samples. Dr. Mattias Johansson, thanks for guiding me through analyses and writing of genetic data. I extend my sincerest thanks to all the scientists and fishermen I had the opportunity to discuss my research with, especially at the Trinational Sardine Forums. Further I thank all the scientists, fisherman and crew that kindly donated their time to collect sardines for this project. Without you my research would not have been possible. I wish to thank all my family and friends that have supported me during my time as a Ph.D. graduate student. In particular: my mother Margaret Baldwin, Nikki and Justin Atkins, Renee Albertson, Amanda Claxton, Dr. Danna Schock, Dawn Hall, my sailing buddies from the YBYC (John and Barbara Dougherty, Ken and Stephanie Brown, Nairne Dickey, Dr. Laurie Weitkamp, Terry Lettenmaier, Jeff Breazile), all the members of the Hatfield Student Organization, the Newport Running Club (Tom and Sheila Swinford, Dennis Pingree and Rebecca Chuck), and all the local ultimate frisbee players. CONTRIBUTION OF AUTHORS Drs. Kym C. Jacobson and Michael A. Banks, my co-advisors, closely advised the planning and execution of this research. Both were involved in editing all the writing, and are therefore coauthors on all four chapters of this dissertation. Mary Beth Rew was involved in data gathering, data analysis and writing of Chapters 3 and 4. Dr. Mattias Johansson assisted with data analysis and writing of Chapter 3. TABLE OF CONTENTS Page GENERAL INTRODUCTION ...................................................................................... 1 Pacific Sardines .......................................................................................................... 2 Trophically-transmitted parasites ............................................................................... 3 Review of methods to assess fish stock structure ....................................................... 5 Identifying migration patterns of Pacific sardines using biological tags ................... 6 Parasite Population Genetics ...................................................................................... 7 Anisakis species ...................................................................................................... 7 Myosaccium ecaude ................................................................................................ 9 Significance of Research .......................................................................................... 11 References ................................................................................................................ 13 Integrating Fish and Parasite Data as a Holistic Solution for Identifying the Ellusive Stock Structure of Pacific sardines (Sardinops sagax) ................................................ 19 Abstract .................................................................................................................... 20 Introduction .............................................................................................................. 21 Fish stock identifications: morphology and artificial tags ....................................... 25 Fish stock identification: molecular markers ........................................................... 28 Recommendations on fish molecular markers ......................................................... 33 Fish stock identification: parasites ........................................................................... 35 Parasite identification and discrimination: morphological and molecular characteristics ........................................................................................................... 37 Recommendations on parasite molecular markers ................................................... 40 TABLE OF CONTENTS (Continued) Page Integrating techniques for fish stock identification .................................................. 41 Conclusion ................................................................................................................ 42 Acknowledgements .................................................................................................. 42 Table ......................................................................................................................... 43 References ...............................................................................................................
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