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Synthesizing Phylogeography and Community Ecology to Understand Patterns of Community Diversity

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Synthesizing Phylogeography and Community Ecology to Understand Patterns of Community Diversity Brigham Young University BYU ScholarsArchive Theses and Dissertations 2021-07-29 Synthesizing Phylogeography and Community Ecology to Understand Patterns of Community Diversity Trevor J. Williams Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Life Sciences Commons BYU ScholarsArchive Citation Williams, Trevor J., "Synthesizing Phylogeography and Community Ecology to Understand Patterns of Community Diversity" (2021). Theses and Dissertations. 9176. https://scholarsarchive.byu.edu/etd/9176 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected]. Synthesizing Phylogeography and Community Ecology to Understand Patterns of Community Diversity Trevor J. Williams A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Jerald B. Johnson, Chair Byron J. Adams Mark C. Belk Seth M. Bybee Lacey L. Knowles Department of Biology Brigham Young University Copyright © 2021 Trevor J. Williams All Rights Reserved ABSTRACT Synthesizing Phylogeography and Community Ecology to Understand Patterns of Community Diversity Trevor J. Williams Department of Biology, BYU Doctor of Philosophy Community ecology is the study of the patterns and processes governing species abundance, distribution, and diversity within and between communities. Likewise, phylogeography is the study of the historic processes controlling genetic diversity across space. Both fields investigate diversity, albeit at different temporal, spatial and taxonomic scales and therefore have varying assumptions. Community ecology typically focuses on contemporary mechanisms whereas phylogeography studies historic ones. However, new research has discovered that both genetic and community diversity can be influenced by contemporary and historic processes in tandem. As such, a growing number of researchers have called for greater integration of phylogeography and ecology to better understand the mechanisms structuring diversity. In this dissertation I attempt to add to this integration by investigating ways that phylogeography and population genetics can enhance studies on community ecology. First, I review traditional studies on freshwater fish community assembly using null model analyses of species co-occurrence, which shows that fish are largely structured by deterministic processes, though the importance of different mechanisms varies across climates, habitats, and spatial scales. Next, I show how phylogeographic data can greatly enhance inferences of community assembly in freshwater fish communities in Costa Rica and Utah respectively. My Costa Rican analyses indicate that historic eustatic sea-level change can be better at predicting community structure within a biogeographic province than contemporary processes. In comparison, my Utah analyses show that historic dispersal between isolated basins in conjunction with contemporary habitat filtering, dispersal limitation, and extinction dynamics both influence community assembly through time. Finally, I adapt a forward-time population genetics stochastic simulation model to work in a metacommunity context and integrate it with Approximate Bayesian Computation to infer the processes that govern observed community composition patterns. Overall, I show that community ecology can be greatly enhanced by including information and methods from different but related fields and encourage future ecologists to further this research to gain a greater understanding of biological diversity. Keywords: Approximate Bayesian Computation, community ecology, dispersal, diversity, habitat filtering, history, metacommunity ecology, phylogeography, population genetics, process-pattern, synthesis ACKNOWLEDGMENTS I first want to thank Jerry, without whom none of this would be possible. His encouragement and advice have helped me grow not just academically, but in all aspects of life. He not only taught me a greater love for the study of evolution and ecology but also how to have fun while doing it. I am also incredibly thankful for Byron, Mark, Seth, and Lacey for all their help in improving my research. Graduate school is challenging, but it would have been even more challenging had it not been for the amazing friends and colleagues I have made along the way. I am especially grateful to my fellow graduate(d) students Scott George, Alli Duffy, Gareth Powell, Ellie Nielsen, Andrea Roth-Monzon, Kaitlyn Golden, Peter Searle, Kevin Lamb, Kandace Flanary, Josh Verde, and Spencer Ingley for their friendship and support. I will never forget my fond memories of congratulatory J-Dawgs and Chub Club adventures. I also want to thank Becca White and the amazing undergraduate students of the Johnson Lab as well as Steve Peck for helping me find my fondness for modeling and theoretical biology. I cannot thank my family enough for their constant support, without which I could never have gotten this far. To the never-ending encouragement of my parents, Winslow and Kristi, and the countless hours of babysitting and emotional support from my siblings, Zach, Paige, and Nathan, their spouses, Janelle, Thomas, and Sariah, and my aunts, Janelle and Carie, all I can say is a heartfelt thank you, and I love you. Finally, and most importantly, I am the most thankful for my amazing wife, Aimee, and my two daughters, Addison and Hadley. You mean all the world to me, and your love helped me through all the ups and downs of this crazy ride. TABLE OF CONTENTS TITLE PAGE ................................................................................................................................... i ABSTRACT .................................................................................................................................... ii ACKNOWLEDGMENTS ............................................................................................................. iii TABLE OF CONTENTS ............................................................................................................... iv LIST OF TABLES ....................................................................................................................... viii LIST OF FIGURES ........................................................................................................................ x CHAPTER ONE: GLOBAL INSIGHTS INTO FRESHWATER COMMUNITY DYNAMICS USING A META-ANALYSIS OF CO-OCCURRENCE NULL MODELS ................................. 1 ABSTRACT ................................................................................................................................ 1 INTRODUCTION ....................................................................................................................... 2 METHODS.................................................................................................................................. 5 Data Collection ........................................................................................................................ 5 Statistical Analyses .................................................................................................................. 8 RESULTS.................................................................................................................................... 9 DISCUSSION ........................................................................................................................... 10 FUTURE DIRECTIONS AND CONCLUSION ...................................................................... 15 ACKNOWLEDGMENTS ......................................................................................................... 16 REFERENCES .......................................................................................................................... 18 CHAPTER TWO: HISTORY PREDICTS COMMUNITY DIVERSIFICATION WITHIN A BIOGEOGRAPHIC PROVINCE OF FRESHWATER FISH BETTER THAN THE ENVIRONMENT OR SPACE ..................................................................................................... 36 ABSTRACT .............................................................................................................................. 36 INTRODUCTION ..................................................................................................................... 37 MATERIALS AND METHODS .............................................................................................. 40 Study System ......................................................................................................................... 40 Data Acquisition .................................................................................................................... 42 Data Analysis ......................................................................................................................... 45 RESULTS.................................................................................................................................. 46 DISCUSSION ........................................................................................................................... 47 Principal Findings .................................................................................................................. 47 Historical Processes Can Affect Local Communities
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