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Molecular Evolutionary and Macroecological Investigations of the Eastern Asian - Eastern North American Floristic Disjunction

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Molecular Evolutionary and Macroecological Investigations of the Eastern Asian - Eastern North American Floristic Disjunction MOLECULAR EVOLUTIONARY AND MACROECOLOGICAL INVESTIGATIONS OF THE EASTERN ASIAN - EASTERN NORTH AMERICAN FLORISTIC DISJUNCTION By ANTHONY ELI MELTON A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2020 © 2020 Anthony Eli Melton To Maddie ACKNOWLEDGMENTS I would like to thank my advisors, Doug and Pam Soltis, for letting me be a part of their academic family for the last five years. They have been incredible in their support and I would not be where I am without them. I would like to thank my committee members, Robert P. Guralnick and Ethan P. White, for their assistance and guidance. I would like to thank everyone, including past members, in the Soltis lab who helped so often on just about everything. I would like to thank my parents for being supportive for all these years. And I would like to thank Maddie McClinton for making all the grad school problems seem insignificant and making every day so much better. I owe many thanks to all the people, from the professors at Montevallo and Auburn to everyone at the University of Florida, who have helped lift me up to where I am today - I wouldn’t be here without your support. During my time at UF, I had the pleasure of working with several amazing undergraduate students whom I would like to thank for all their work. I would like to thank the National Science Foundation, the American Society of Plant Taxonomists, the Botanical Society of America, and UF Biology Department and Graduate Student Association for funding for research and travel. I would also like to acknowledge and thank the many collaborators I have worked with during my time at the University of Florida. Shichao Chen, Yunpeng Zhao, Chengxin Fu, Qiu- Yun (Jenny) Xiang, Shifeng Cheng, and Gane K.-S. Wong helped collect leaf samples, perform RNA extractions, and sequencing and assembly of transcriptomes used for analyses in Chapter 2. I would like to thank Matthew H. Clinton, Donald N. Wasoff, Limin Lu, Haihua Hu, Zhiduan Chen, and Keping Ma for assistance in acquiring occurrence data and preliminary analyses using ecological niche modeling for Chapter 3. I would like to thank Hanyang Lin, Miao Sun, William M. Whitten, Michelle Mack, Stephanie Bohlman, Sarah Graves, Yuhnpeng Zhou, Chengxin Fu, 4 Jeremy Lichstein, and Robert P. Guralnick for collecting plant samples and functional trait data and helping develop the functional diversity analyses used in Chapter 4. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS ...............................................................................................................4 LIST OF TABLES ...........................................................................................................................8 LIST OF FIGURES .......................................................................................................................10 ABSTRACT ...................................................................................................................................11 CHAPTER 1 INTRODUCTION ..................................................................................................................13 2 COMPARISONS OF RATES OF MOLECULAR EVOLUTION IN EASTERN ASIAN AND EASTERN NORTH AMERICAN DISJUNCT PLANT SPECIES ................17 Background .............................................................................................................................17 Methods ..................................................................................................................................19 Sample Selection, Tissue Processing, Transcriptome Assembly, and Ortholog Selection .......................................................................................................................19 Codeml Analyses .............................................................................................................21 Post-Codeml Statistical Analyses ....................................................................................22 Results.....................................................................................................................................23 Pipeline Output ................................................................................................................23 Pairwise Analyses ............................................................................................................24 Per-branch Analyses ........................................................................................................24 GO Categories .................................................................................................................25 Discussion ...............................................................................................................................26 3 CLIMATIC NICHE COMPARISONS OF EASTERN ASIAN AND EASTERN NORTH AMERICAN DISJUNCT PLANT SPECIES ..........................................................40 Background .............................................................................................................................40 Methods ..................................................................................................................................42 Occurrence Data Processing ............................................................................................42 Climatic Data Processing ................................................................................................43 Ecological Niche Model Development ...........................................................................44 Analyses ..........................................................................................................................45 Results.....................................................................................................................................46 Discussion ...............................................................................................................................48 4 NICHE FILLING DYNAMICS OF EASTERN ASIAN AND EASTERN NORTH AMERICAN WOODY PLANT COMMUNITIES ................................................................57 Background .............................................................................................................................57 6 Methods ..................................................................................................................................59 Sampling ..........................................................................................................................59 Trait Analyses ..................................................................................................................60 Functional Diversity Calculations ...................................................................................61 Results.....................................................................................................................................62 Discussion ...............................................................................................................................64 5 CONCLUSIONS ....................................................................................................................71 APPENDIX A CHAPTER TWO SUPPLEMENTARY MATERIAL ...........................................................74 B CHAPTER THREE SUPPLEMENTARY MATERIAL .....................................................112 C CHAPTER FOUR SUPPLEMENTARY MATERIAL .......................................................126 LIST OF REFERENCES .............................................................................................................128 BIOGRAPHICAL SKETCH .......................................................................................................143 7 LIST OF TABLES Table page 2-1 This table includes all species included in the study, the region in which it occurs, and mean for dN, dS, and dN/dS () scores. ......................................................................33 3-1 Regional means per genus for estimated distribution size, niche breadth (B1 and B2), hypervolumes (HV), and mean climatic niche widths (mean annual temperature and annual precipitation) per genus. .........................................................................................52 4-1 Summary of diversity statistics for whole PAM functional diversity analyses. ................70 A-1 Voucher information for all plant specimens used in this study. ......................................76 A-2 Gene number and mean, median, and standard deviation (SD) for scores for each species included. ................................................................................................................77 A-3 t-test statistics, including 95% confidence intervals (CI), for pairwise comparisons (excluding Liriodendron) of the log of dN, dS, and dN/dS scores for entire gene sets......80 A-4 ANOVA results for Liriodendron. .....................................................................................81 A-5 Results for Dunn’s pairwise test (ad-hoc test for Kruskal-Wallis test) for Calycanthus........................................................................................................................82 A-6 Results for Dunn’s pairwise test for all Cornus branch comparisons. ...............................83 A-7 Results for Dunn’s pairwise test for all Hamamelis branch comparisons. ........................87
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