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Functional Genetics of Eastern Oysters ( Crassostrea Virginica ) Across Salinity Variation in a Single Estuary

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Functional Genetics of Eastern Oysters ( Crassostrea Virginica ) Across Salinity Variation in a Single Estuary FUNCTIONAL GENETICS OF EASTERN OYSTERS ( CRASSOSTREA VIRGINICA ) ACROSS SALINITY VARIATION IN A SINGLE ESTUARY A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Laura Elizabeth Eierman May 2014 © 2014 Laura Elizabeth Eierman FUNCTIONAL GENETICS OF EASTERN OYSTERS ( CRASSOSTREA VIRGINICA ) ACROSS SALINITY VARIATION IN A SINGLE ESTUARY Laura Elizabeth Eierman, Ph. D. Cornell University 2014 Understanding the interaction between selection and phenotypic plasticity is important for predicting species’ persistence in rapidly changing environments. For sessile organisms, phenotypic plasticity is a typical mechanism for responding to environmental variation. However, the additional characteristics of high fecundity and widely dispersing offspring present an opportunity for selection to reshape the functional genetic composition of populations across habitat heterogeneities every generation. I tested for this pattern of recurrent viability selection in eastern oysters, Crassostrea virginica, using two experimental approaches. First, I made within- reef pair crosses from low, intermediate and high salinity source oysters and analyzed larval survival after a ten day exposure to 10 and 30 salinity treatments. The parental reef source-by- larval salinity treatment interaction term was a significant predictor of larval survival. Second, I sequenced and assembled the oyster transcriptome de novo in order to conduct RNA-seq to identify differential gene expression patterns in response to salinity treatment and oyster reef source. The samples for RNA-seq were twenty-four adult oysters collected from high and low salinity source reefs and acclimated for 9 weeks in 10 and 30 salinity common gardens. A total of 9,921 reference transcriptome contigs (reftigs; 23.6%) were significantly differentially expressed (DE), with 0.6% of all reftigs DE for the reef source, 18.9% DE for treatment salinity, and 13.9% DE for the reef-by-treatment factor. The reftigs responding to treatment and the reef- by-treatment factors demonstrate a genomically pervasive pattern of plastic gene expression in response to salinity. Additionally, the abundant genotype-by-environment patterns suggest that the history of selection at each reef is generating different plastic responses after acclimation to the same osmotic condition. Overall, the reef-specific patterns of gene expression and larval survival indicate that oyster responses to habitat heterogeneity are shaped by both phenotypic plasticity and recurrent viability selection. Furthermore, the larval results suggest that the functional plasticity differences observed in the adults were heritable. Studies on the interaction between plasticity and evolutionary responses typically classify plasticity as acting within generations and selection as acting between generations. I suggest that for high dispersal species with type III survivorship, intra-generational selection can shape patterns of plasticity across habitats. BIOGRAPHICAL SKETCH Laura Elizabeth Eierman was born in Jarrettsville, MD and was raised by her parents, Frederick and Roberta, along with her sister Elaine. When she was two years old, her grandfather, Howard Vonderheide, spent an entire day coaxing her into the water at Ocean City, MD. After that first introduction to the waves, Laura fell in love with the ocean, and she decided early on to become a marine scientist. She attended Salisbury University in Salisbury, MD, graduating summa cum laude within the Bellavance Honor’s program in 2002. She dual majored in Biology and Environmental Science with a concentration in Marine Science and a minor in Chemistry. Laura immediately began a Master of Science in Marine Biology at the University of Massachusetts, Dartmouth where she was advised by Dr. Richard Connor. She spent three years studying wild dolphin foraging behavior and habitat selection along with fish communities and acoustics at Turneffe Atoll, Belize. Following the completion of her MS degree, Laura proceeded to teach general science at Sparrows Point Middle School in Baltimore County, MD while earning a Master of Arts in Teaching at Towson University. She started a school-wide environmental club and recycling program. She was awarded the TABCO Rookie of the Year teaching award in 2006. During her time as a teacher, Laura was blessed to live across the street from her grandmother, Roberta Vonderheide. After teaching for two years, Laura began a PhD program in Natural Resources at Cornell University in the fall of 2007. During the past seven years, she has pursued both her passion for marine conservation through her research on eastern oysters and her love of teaching. After completing her degree, Laura plans to work in academia, teaching at the undergraduate level while providing her students with research opportunities. v Dedicated to all of the teachers in my life vi ACKNOWLEDGMENTS I could not have completed this dissertation without the support, guidance, patience and generosity of many people. First, I would like to thank my committee chair, Dr. Matthew Hare. I first met Matt at the University of Maryland, College Park in October, 2006. We discussed my research interests and the skills I wanted to improve through my PhD work. At the end of the meeting, Matt shook my hand and said, “It was a pleasure talking with you.” Unlike other potential advisors I had met, Matt was sincere. I knew immediately that if he offered me a position as a graduate student, I would say yes. Over the course of my time at Cornell, Matt has met with me weekly, given me guidance, and asked me the hard questions to help me and this project be the best possible. He is a true mentor. My committee members have also been a great support. Before my first semester began, I knocked on Dr. Patrick Sullivan’s door and said, “I am going to need a lot of help with statistics.” Due to Pat’s guidance and extraordinary patience, I now have a thorough understanding of statistics. Additionally, Dr. Jim Morin and Dr. Brian Lazzaro have provided invaluable feedback, particularly regarding the scope of the second and third papers. I would like to thank both of my research assistants, Hilary Kates (summer 2010) and Katie Kirk (summer 2011). They provided invaluable help during field work, and they valiantly made it through long nights of spawning oysters and counting larvae. They also made our time in the field enjoyable through trips to the beach, movie nights, and excursions to find ice cream. Additionally, I would like to acknowledge the generosity of Dr. John Scarpa, the staff at Harbor Branch Oceanographic Institute, Dr. David Bushek and the staff at Haskin Shellfish Research Laboratory. Both Dr. Scarpa and Dr. Bushek kindly provided me with hatchery space at their respective facilities for my larval experiment, and they shared their expertise while I learned how to condition and spawn oysters. vii Also, thank you to Dr. Willie Fetzer and Dr. Suzy Strickler. During a chat with Willie about data analysis, he brought up the ‘survival’ R package as a potential means for analyzing my larval survival data. Suzy graciously shared a custom pipeline for calculating dN/dS ratios between sequences and helped me troubleshoot the pipeline for use with my data. Graduate programs are intense and the community of people in your life makes all of the difference. I am grateful for the camaraderie of the Hare Lab members. Harmony Borchardt- Wier provided guidance through the nitty gritty of lab protocol. The undergraduates, particularly Courtney Verscaj, were helpful in completing analyses. Finally, Catherine Sun has been one of the best lab mates anyone could ask for. We have brainstormed, vented, run half marathons, and consumed a lot of coffee together. Cat, thank you for everything. Additionally, the graduate students of DNR are a family, supporting and cheering each other on. I would like to specifically thank Laura Martin and Taza Schaming, two members of my cohort. Their friendship from the first day we started at Cornell University has kept me going all of these years. Finally, a huge heart-felt thank you to my family and friends. Daisy Kaplan has been one of my closest friends since we met at UMASS Dartmouth in 2002. A fellow PhD student, Daisy has been the friend who “gets it” without having to explain, and has regularly served as a diversion with stories of her adventures in Manhattan. My childhood friends, April, Rebecca and Adrienne, have remained close, visiting me over the years and keeping me grounded. Thank you to my parents who have been my greatest supporters. They have stopped what they were doing for every phone call, and they have visited whenever I have needed company or help. In general, they have been the parents that every graduate student should have. Thank you to my sister and her family - Drew, Molly and Brody - who have been a refreshing break from school and research. Thank you to my grandma, who is always happy to listen and cheer me on. Finally, thank you to Scott Flickinger. Scott has been the most immediate person in my life during my viii PhD: the person who sat on the couch next to me while I studied for my A exam and the person who got the first phone call when I passed my B exam. Scott, thank you for your patience while I pursued my PhD, and ultimately, thanks for making me laugh during the ride. ix TABLE OF CONTENTS BIOGRAPHICAL SKETCH ..........................................................................................................v
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