Genetic Evaluation of American Shad Alosa Sapidissima Restoration Success in James River, Virginia

Virginia Commonwealth University VCU Scholars Compass

Theses and Dissertations Graduate School

2010

Genetic evaluation of American shad Alosa sapidissima restoration success in James River, Virginia

Aaron Aunins Virginia Commonwealth University

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This Dissertation is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. GENETIC EVALUATION OF AMERICAN SHAD ALOSA SAPIDISSIMA RESTORATION SUCCESS IN JAMES RIVER, VIRGINIA

A dissertation submitted in partial fulﬁllment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University

AARON WILLIAM AUNINS Bachelor of Arts B.A., University of Richmond, 2001

Master of Science M.S., College of William and Mary, 2006

Major Professor: BONNIE L. BROWN, PH.D. Professor, Department of Biology Virginia Commonwealth University Richmond, Virginia August, 2010 c Aaron William Aunins 2010 All Rights Reserved Integrative Life Sciences Virginia Commonwealth University This page certiﬁes that the dissertation prepared by Aaron W. Aunins entitled “Genetic evaluation of American shad Alosa sapidissima restoration success in James River, Virginia” has been approved by his committee as satisfactory completion of the thesis requirement for the degree of Doctor of Philosophy in Integrative Life Sciences.

Bonnie L. Brown, Ph.D., Professor, Department of Biology, College of Humanities and Sci- ences

Rodney J. Dyer, Ph.D., Associate Professor, Department of Biology, College of Humanities and Sciences

Edward L. Boone, Ph.D., Assistant Professor, Department of Statistical Sciences and Oper- ations Research, College of Humanities and Sciences

John M. Epifanio, Ph.D., Professional Scientist, Illinois Natural History Survey

Peter E. Smouse, Ph.D., Professor II, Rutgers University

Robert M. Tombes, Ph.D., Director, Integrative Life Sciences

Thomas F. Huﬀ, Ph.D., Vice Provost of Life Sciences

F. Douglas Boudinot, Ph.D., Dean of the Graduate School ii

ACKNOWLEDGEMENTS

Completion of this dissertation would not have been possible without the help and sup- port of many individuals. First, I acknowledge my major advisor, Dr. Bonnie Brown. Dr. Brown was a constant source of encouragement throughout all stages of this project, and has always been there to answer my questions without hesitation. Not only have I learned a lot about conservation genetics from her, but she has taught me how population genetics and molecular techniques in general are useful for addressing a wide range of biological problems. I thank my committee members Dr. Smouse, Dr. Epifanio, Dr. Boone, and Dr. Dyer. I am honored to have had Dr. Smouse on my committee, and his expertise in mixed-stock analyses was indispensible. Dr. Epifanio always had good suggestions for how to approach the mixed-stock analysis problem, and was always supportive of all my eﬀorts. Dr. Boone taught me a great deal about Bayesian data analyses, and introduced me to type-setting documents in LATEX. Dr. Dyer tolerated me popping into his oﬃce un-announced on several occasions with random R questions, or just to talk about Sciroccos and bee-keeping. In addition, I learned a lot from his population genetics class. Funding for the genetics study was provided by the Virginia Department of Game and In- land Fisheries, and the Federal Aid in Sport Fish Restoration Program. The radio telemetry study was funded by the Fish America Foundation, and the U.S. Fish and Wildlife Service. In addition, I received tuition and stipend su