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Open Parkinson Dissertation Final The Pennsylvania State University The Graduate School Eberly College of Science THE ROLE OF INTRASPECIFIC DIVERSITY IN CORAL-ALGAL SYMBIOSIS ECOLOGY AND EVOLUTION A Dissertation in Biology by John Everett Parkinson 2014 John Everett Parkinson Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2014 The dissertation of John Everett Parkinson was reviewed and approved* by the following: Iliana B. Baums Associate Professor of Biology The Pennsylvania State University Dissertation Advisor Todd C. LaJeunesse Associate Professor of Biology The Pennsylvania State University Chair of Committee Mary Alice Coffroth Professor of Evolution, Ecology, and Behavior State University of New York at Buffalo Special Signatory Istvan Albert Associate Professor of Bioinformatics The Pennsylvania State University James H. Marden Professor of Biology The Pennsylvania State University Andrew F. Read Professor of Biology The Pennsylvania State University Douglas R. Cavenar Professor of Biology The Pennsylvania State University Department Head of Biology *Signatures are on file in the Graduate School iii ABSTRACT Coral-algal mutualisms, the foundation of reef ecosystems, can break down during periods of thermal stress. The extent to which such partnerships may acclimate or evolve to survive a changing climate is poorly understood. Though evolutionary responses are driven by the natural selection of functional variation among individuals within species, such variation has been difficult to quantify in coral systems. Here, I use high-resolution molecular techniques to differentiate individuals, populations, and species within coral symbioses and subsequently quantify the ecological and evolutionary relevance of intraspecific variation. In the first chapter, I review the technological advances that have made such work possible, and describe preliminary data from several researchers indicating that intraspecific variation may be extensive among coral hosts and symbionts. In the second chapter, I test the value of manipulating coral-algal partnerships during host larval development for restoration purposes, finding little influence of symbiont identity on growth rates during early ontogeny. In the third chapter, I formally describe several new species of Symbiodinium, the morphologically cryptic dinoflagellate endosymbionts that associate with cnidarians, and draw attention to the ecological diversity that can be found even among closely-related groups. In the fourth chapter, I characterize molecular variation among individuals of the coral Acropora palmata that affects the photochemistry of a clonal symbiont responding to thermal stress, emphasizing that fine scale partner interactions can yield functional variation among coral holobionts with potential evolutionary consequences. In the fifth chapter, I compare gene content and steady-state expression among several closely related Symbiodinium within the Clade B lineage, identifying phylogenetic and ecological transcriptional signatures among species. This work represents a few first steps into the complex and exciting territory of fine scale variation among marine mutualisms. iv TABLE OF CONTENTS List of Figures .......................................................................................................................... vi List of Tables ........................................................................................................................... xii Acknowledgements .................................................................................................................. xiv Chapter 1 THE EXTENDED PHENOTYPES OF MARINE SYMBIOSES: ECOLOGICAL AND EVOLUTIONARY CONSEQUENCES OF INTRASPECIFIC GENETIC DIVERSITY IN CORAL-ALGAL ASSOCIATIONS. ... 1 Abstract ............................................................................................................................ 1 Introduction ...................................................................................................................... 2 Acknowledgements .......................................................................................................... 32 Figures .............................................................................................................................. 33 References ........................................................................................................................ 41 Chapter 2 LIMITED BENEFIT OF LARVAL SYMBIONT MANIPULATION FOR EX SITU CORAL RESTORATION ...................................................................................... 68 Abstract ............................................................................................................................ 68 Introduction ...................................................................................................................... 69 Materials and Methods ..................................................................................................... 72 Results .............................................................................................................................. 75 Discussion ........................................................................................................................ 77 Acknowledgements .......................................................................................................... 81 Figures .............................................................................................................................. 83 References ........................................................................................................................ 88 Chapter 3 THE MOLECULAR, ECOLOGICAL, AND TAXONOMIC DIVERSITY OF SYMBIODINIUM (DINOPHYCEAE) CLADE B IN THE NORTHWESTERN ATLANTIC OCEAN, INCLUDING DESCRIPTIONS OF S. AENIGMATUM SP. NOV., S. ANTILLOGORGIA SP. NOV., S. BRIAREUM SP. NOV., S. MADRACIS SP. NOV., AND S. PSEUDOMINUTUM SP. NOV. ....................................................... 97 Abstract ............................................................................................................................ 97 Introduction ...................................................................................................................... 98 Materials and Methods ..................................................................................................... 101 Results .............................................................................................................................. 103 Discussion ........................................................................................................................ 109 Acknowledgements .......................................................................................................... 115 Figures .............................................................................................................................. 116 References ........................................................................................................................ 124 v Chapter 4 INTRASPECIFIC DIVERSITY AMONG HOST-SYMBIONT PAIRINGS YIELDS FUNCTIONAL VARIATION IN CORAL-ALGAL SYMBIOSES ................ 132 Abstract ............................................................................................................................ 132 Introduction ...................................................................................................................... 133 Materials and Methods ..................................................................................................... 135 Results .............................................................................................................................. 141 Discussion ........................................................................................................................ 145 Acknowledgments ............................................................................................................ 151 Figures .............................................................................................................................. 153 References ........................................................................................................................ 164 Chapter 5 SYMBIODINIUM TRANSCRIPTION VARIES EXTENSIVELY AMONG INDIVIDUALS AND SPECIES WITHIN CLADE B. ................................................... 175 Abstract ............................................................................................................................ 175 Introduction ...................................................................................................................... 176 Methods ............................................................................................................................ 179 Results .............................................................................................................................. 185 Discussion ........................................................................................................................ 188 Acknowledgements .......................................................................................................... 196 Figures .............................................................................................................................. 197 References .......................................................................................................................
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