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The Role of Evolution in Maintaining Coexistence of Competitors Abigail I Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2017 The Role of Evolution in Maintaining Coexistence of Competitors Abigail I. (Abigail Ilona) Pastore Follow this and additional works at the DigiNole: FSU's Digital Repository. For more information, please contact [email protected] FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES THE ROLE OF EVOLUTION IN MAINTAINING COEXISTENCE OF COMPETITORS By ABIGAIL I. PASTORE A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy 2017 Copyright c 2017 Abigail I. Pastore. All Rights Reserved. Abigail I. Pastore defended this dissertation on August 4, 2017. The members of the supervisory committee were: Thomas Miller Professor Directing Dissertation Richard Bertram University Representative Brian Inouye Committee Member Scott Steppan Committee Member Alice Winn Committee Member The Graduate School has verified and approved the above-named committee members, and certifies that the dissertation has been approved in accordance with university requirements. ii For my Mom and for Kristofer Ad astra per aspera iii ACKNOWLEDGMENTS Tom Miller can not be thanked enough, he is a beacon of patience, generosity and fun. His intellec- tual guidance is pervasive through this document and this work should be seen as an extension of the Miller legacy of evolution among competitors. My committee members were aces; Alice Winn's keen ability to cut straight to the heart of any bullshit and generally bring joviality into my day, Scott Steppan's expert guidance through a milieu of phylogenetic inference and general supporter of my stage presence. Brian Inouye's expertise in maximum likelihood estimation and bike mechanic skills were clutch. Thanks to Richard Bertram's ability to bend my conceptual understanding into dimensions I wasn't recognizing. Olivia Mason gave me the keys to the black box of bacterial ecology, and patiently helped me turn the locks. Charlotte Lee helped me struggle through coexistence theory and generally expanded my understanding of competition theory. All of the FSU E and E Faculty members have been delightful and intellectually invigorating including Don Levitan, Nora Underwood, David Houle, Kim Hughes, and Janey Wolfe. The E and E graduate students and post docs were the most supportive and fun people I've ever been around, particularly thanks to Wilbur Ryan and Andrew Merwin for always being down for a debate or a song. Elise Gornish and Josh Grinath's guidance in my early years certainly should not go unrecognized. Casey terHorst and Catalina Cuellar-Gempler were also fantastic mentors. When I started grad school I had no idea I'd leave with such a big and wonderful family. But this would not have been possible without my biological family. My mom is the most supportive, loving and generous person I know. My dad instilled a sense of adventure and love of the natural world within me. Veronica is my rock and her seemingly endless support and encouragement were exactly what I needed to keep going more times than I can count. Omi and Opa, Kevin and Solara are my biggest cheer leaders. My aunts, uncles and cousins are just the best, and knowing I had such a loving and accepting family behind me helped me keep striving. I am awestruck that I am so blessed to have two big and wonderful families to support me on this journey. Thanks to Fallon Ringer for helping me develop the coping skills to finish strong. Undergraduate researchers that were tremendously helpful, fun and insightful include; Henry Gwynn, Pamela Betancourt, Deniece Wade, Tom Thornburg, Kennedy Wohlgemuth and Matthew iv Green. Peter Adler, Nelson Hairston Jr., Doug Schemske, and Priyanga Amarasekare provided stimulating conversations that improved this work. Funding from the Florida State University Biology Department, Florida State University and the National Science Foundation's Doctoral Dissertation Improvement Grant. Many thanks to Ruth Didier for troubleshooting flow cytometry methods and the FSU College of Medicine for use of the flow cytometer. Thanks to Sarah Owens and Argonne National Lab for library prep and illumina runs of the 16S bacterial samples. v TABLE OF CONTENTS List of Tables . viii List of Figures . ix Abstract . xiv 1 Introduction 1 1.1 Summary of Goals . 1 1.2 Background . 1 1.3 Outline . 4 2 Theoretical Evidence for the Role of Evolution in Competitor Coexistence 7 2.1 Introduction . 7 2.2 Model and Methods . 8 2.3 Results . 11 2.4 Discussion . 17 2.5 Conclusions . 19 3 Phylogenetic Signal does not Predict Competitive Interactions in Protist Mi- crocosms 20 3.1 Introduction . 20 3.2 Methods . 22 3.2.1 Protist Cultures . 22 3.2.2 Quantifying Competition . 23 3.2.3 Quantifying Protist Traits . 24 3.2.4 Quantifying Phylogenetic Distance . 24 3.3 Results . 26 3.4 Discussion . 28 3.4.1 Conclusions . 36 4 Evidence for the Role of Evolution in Competitor Coexistence in Protist Micro- cosms 37 4.1 Introduction . 37 4.2 Methods . 39 4.2.1 Bacterial Broth . 39 4.2.2 Protist Cultures . 39 4.2.3 Preparation of Stock Lines for Experiment . 40 4.2.4 Selection Experiment . 41 4.2.5 Response Surface Experiments . 41 4.2.6 Invasion Experiments . 43 4.2.7 Estimating Niche Overlap and Fitness Differences . 43 4.3 Results . 43 4.3.1 T etrahymena vs Colpoda ............................. 43 vi 4.3.2 T etrahymena vs Maryna ............................. 46 4.3.3 Maryna vs P aramecium ............................. 51 4.3.4 Invasibility . 56 4.4 Discussion . 56 4.4.1 Conclusions . 59 5 Evolution of Bacterial Consumption in Competing Protists 60 5.1 Introduction . 60 5.2 Methods . 62 5.2.1 Bacterial Broth . 62 5.2.2 Protist Cultures . 64 5.2.3 Preparation of Stock Lines for Experiment . 64 5.2.4 Selection Experiment . 65 5.2.5 Measuring Effect of Protists on the Bacterial Community. 65 5.2.6 Flow Cytometry . 66 5.2.7 Metagenomic Sequencing . 66 5.3 Results . 68 5.3.1 Effects on Bacterial Abundances . 68 5.3.2 Effects on Bacterial Community Composition . 68 5.4 Discussion . 73 6 Concluding Remarks 78 Bibliography . 81 Biographical Sketch . 90 vii LIST OF TABLES 3.1 Day 5: Table of interaction coefficients, ICij. Were column species are species, j, which effect the row species, i. Signicant differences between density of species in monocultures vs. competition are indicated. + p < 0:1, * p < 0:05, ** p < 0:01, *** p < 0:001. 26 3.2 Day 46: Table of interaction coefficients, ICij. Were column species are species, j, which effect the row species, i. Signicant differences between density of species in monocultures vs. competition are indicated. + p < 0:1, * p < 0:05, ** p < 0:01, *** p < 0:001. 28 4.1 t-statistics and P-values from multiple linear regression of the effect of each species density on the per-capita growth rate of the focal species. 44 4.2 t-statistics and P-values from multiple linear regression of the effect of each species density on the per-capita growth rate of the focal species. 46 4.3 t-statistics and P-values from multiple linear regression of the effect of each species density on the per-capita growth rate of the focal species. 50 5.1 F-statistics and P-values for permanovas of the effects of protists on bacterial com- position over time. Time is 0 hours or 9 hours, treatments are bacterial broth, and species lines. After selection, each species has a line selected in monoculture and in pairwise competition. 70 viii LIST OF FIGURES 1.1 The balance between niche overlap and fitness difference among competitors deter- mines outcomes of competition. Small fitness differences equalize competitors, whereas large niche difference stabilize population dynamics. When niche overlap is large, species must be similar in their fitness in order to coexist. (reproduced from Adler et al. 2007). 3 2.1 Three examples of how niche overlap and fitness differences change as a result of se- lection on the trait values of two competitors. Each point on the graph is a starting condition and vectors indicate the direction and relative magnitude of changes in niche and fitness differences (scaled down for illustration). The gray areas are regions in which one species will be competitively excluded, whereas the white region indicates coexistence between species. Red arrows represent areas where species originally co- existed, but evolution changed the ecological outcome to competitive exclusion. Blue regions represent where species would undergo competitive exclusion if only ecological dynamics were occurring, but species evolved in ways that allowed coexistence be- fore exclusion occurred. The sigma value indicates the breadth of the environmental landscape; species are more likely to evolve to coexist in environments with a broader environmental niche breadth. 12 2.2 The initial niche overlap of the two species predicts the final niche overlap of two competing species (for the parameters shown here: r2 = 0:67; p < 0:001). The grey area represents divergence in the species niches, and the white area represents conver- gence in the species niches. Where the linear regression intersects the shaded region, no change in niche overlap is predicted as a consequence of evolutionary dynamics, referred to subsequently as the evolutionarily stable value of niche overlap (H2 = 0:1, σ = 0:2)............................................ 13 2.3 The breadth of the resource environment determines how tightly species will pack after evolving in trait values in response to competition. The vertical dashed line is the trait variance of both species. When intraspecific variance of species is equal to the breadth of the environment, species maximize niche overlap. A. The evolutionarily stable value of niche overlap (see Fig.
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