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University of California, Merced UNIVERSITY OF CALIFORNIA, MERCED The ecological and evolutionary effects of environmental perturbations on populations and communities A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Quantitative and Systems Biology by Holly Frances Swift Committee in charge: Dr. Michael N Dawson, Advisor-Chair Dr. Jessica L. Blois Dr. Marilyn Fogel Dr. Steven H. D. Haddock Dr. Mark D. Ohman 2016 © Copyright Holly F. Swift, 2016 All rights reserved. The dissertation of Holly F. Swift is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Michael N Dawson, Advisor-Chair Jessica Blois Marilyn Fogel Steven Haddock Mark D. Ohman University of California, Merced 2016 iii DEDICATION To my Apodidae family and my little Artemisia “The mountains are calling…” All my love iv EPIGRAPH The brook would lose its song if we removed all the rocks Wallace Stegner The spaces between the stars are where the work of the universe is done Ivan Doig I must go down to the seas again, for the call of the running tide Is a wild call and a clear call that may not be denied… John Mansefield, Sea Fever v TABLE OF CONTENTS List of Figures................................................................................................................... ix List of Tables ................................................................................................................... xv List of Appendices…………………………………………………………………….xvii Acknowledgements ......................................................................................................... xx Curriculum Vitae.......................................................................................................... xxii Abstract........................................................................................................................ xxvii Chapter 1: Introduction – Applying eco-evolutionary dynamics in the pelagic realm ........................................................................................................................................... 28 1 Context.................................................................................................................. 28 2 Dissertation Objectives......................................................................................... 30 3 References............................................................................................................. 31 4 Figures................................................................................................................... 35 Chapter 2: Three routes to crypsis: Stasis, convergence, and parallelism in the Mastigias species complex (Scyphozoa, Rhizostomeae) .............................................. 37 1 Abstract................................................................................................................. 37 2 Introduction........................................................................................................... 37 3 Methods................................................................................................................. 40 3.1 Study region and system ................................................................................. 40 3.2 Molecular analyses: extraction, amplification, sequencing and alignment .... 40 3.3 Molecular analyses: phylogenetic reconstruction and intraspecific networks 41 3.4 Morphological analyses.................................................................................. 43 3.4.1 Specimen collection.................................................................................. 43 3.4.2 Morphological measurements................................................................... 43 3.4.3 Construction of data matrices ................................................................... 43 3.4.4 nMDS analyses......................................................................................... 44 3.5 Hypothesis testing, character state reconstruction & phylogenetic contrasts. 45 4 Results................................................................................................................... 45 4.1 Phylogenetic analyses..................................................................................... 45 4.2 Morphological analyses.................................................................................. 46 4.3 Hypothesis testing, character state reconstruction, & phylogenetic contrasts 47 vi 5 Discussion............................................................................................................. 48 5.1 Hypothesis evaluation..................................................................................... 48 5.2 Three routes to crypsis.................................................................................... 48 5.2.1 Crypsis through stasis ................................................................................. 49 5.2.2 Crypsis through convergence.................................................................... 50 5.2.3 Crypsis through parallelism ...................................................................... 50 5.3 Implications for understanding crypsis in the seas ......................................... 52 6 References............................................................................................................. 53 7 Tables & Figures................................................................................................... 61 Chapter 3: environmental and density related variations in morphology and behavior despite genetic similarity in a gelatinous zooplankton – Mastigias papua 82 1 Abstract................................................................................................................. 82 2 Introduction........................................................................................................... 82 3 Methods................................................................................................................. 84 3.1 Study system................................................................................................... 84 3.2 Genetic Analyses............................................................................................ 84 3.3 Morphological Analyses................................................................................. 86 3.4 Behavioral Analyses....................................................................................... 87 4 Results................................................................................................................... 88 4.1 Genetic Analyses............................................................................................ 88 4.2 Morphological Analyses................................................................................. 88 4.3 Behavioral Analyses....................................................................................... 89 5 Discussion............................................................................................................. 89 5.1 Sources of variation ........................................................................................ 90 5.2 Ecological implications of morphological and behavioral variation .............. 91 5.3 Implications for environmental variability research on medusozoans and marine systems.......................................................................................................... 92 6 References............................................................................................................. 93 7 Tables & Figures................................................................................................... 99 Chapter 4: environmental causes and synecological consequences of dramatic fluctuations in Mastigias (Scyphozoa, Rhizostomeae) population size .................... 114 1 Abstract............................................................................................................... 114 2 Introduction......................................................................................................... 114 3 Methods............................................................................................................... 116 3.1 Study system................................................................................................. 116 3.2 Data Collection............................................................................................. 116 3.3 Data Analyses............................................................................................... 118 4 Results................................................................................................................. 119 vii 5 Discussion........................................................................................................... 121 5.1 Processes controlling Mastigias population size........................................... 121 5.2 Synecological consequences of Mastigias population fluctuations.............. 122 5.3 Broader Implications..................................................................................... 123 6 References........................................................................................................... 124 7 Tables & Figures................................................................................................. 128 Chapter 5: Conclusion – Application of eco-evolutionary dynamics in the pelagic marine realm ................................................................................................................
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