EVOLUTIONARY ECOLOGY OF RIBOSOMAL RNA COPY NUMBER: STUDIES IN SOIL PROKARYOTE AND NEMATODE COMMUNITIES by Mark Reid Williamson Bachelor of Science, University of North Dakota, 2014 A Dissertation Submitted to the Graduate Faculty of the University of North Dakota in partial fulfillment of the requirements for the degree of Doctor of Philosophy Grand Forks, North Dakota December 2019 PERMISSION Title Evolutionary Ecology of Ribosomal RNA Copy Number: Studies in Soil Prokaryote and Nematode Communities Department Biology Degree Doctor of Philosophy In presenting this dissertation in partial fulfillment of the requirements for a graduate degree from the University of North Dakota, I agree that the library of this University shall make it freely available for inspection. I further agree that permission for extensive copying for scholarly purposes may be granted by the professor who supervised my dissertation work or, in her/his absence, by the Chairperson of the department or the Dean of the Graduate School. It is understood that any copying or publication or other use of this dissertation or part thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of North Dakota in any scholarly use which may be made of any material in my dissertation. Mark R. Williamson December 5th, 2019 iii TABLE OF CONTENTS LIST OF FIGURES………………………………………………………………………………………viii LIST OF TABLES .......................................................................................................................ix ACKNOWLEDGEMENTS .........................................................................................................x ABSTRACT ............................................................................................................................... xi CHAPTER I. ECOLOGY, EVOLUTION, AND GENOMICS IN THE SOIL ENVIRONMENT ......................................................................... 1 Soil Health Monitoring ......................................................................................... 1 Ecological Stoichiometry ...................................................................................... 3 Growth Rate Hypothesis ....................................................................................... 5 Genetic Hypotheses for the Growth Rate Hypothesis .......................................... 6 Ribosomal RNA .................................................................................................... 10 Copy Number Variation ........................................................................................ 10 Prokaryotes ........................................................................................................... 12 Nematodes............................................................................................................. 13 Maturity Index ...................................................................................................... 14 Objectives ............................................................................................................. 16 II. PHYLOGENETIC AUTOCORRELATION ........................................................ 22 Abstract ................................................................................................................. 22 Introduction ........................................................................................................... 22 Objectives ............................................................................................................. 24 Methods................................................................................................................. 24 Results ................................................................................................................... 28 Discussion ............................................................................................................. 31 Conclusion ............................................................................................................ 35 III. OAKVILLE PRAIRIE SOIL CORE STUDIES ................................................... 51 Abstract ................................................................................................................. 51 iv Introduction ........................................................................................................... 51 Objectives ............................................................................................................. 55 Methods................................................................................................................. 55 Results ................................................................................................................... 62 Discussion ............................................................................................................. 66 Conclusion ............................................................................................................ 71 IV. KONZA PRAIRIE SOIL STUDIES ..................................................................... 86 Abstract ................................................................................................................. 86 Introduction ........................................................................................................... 86 Objectives ............................................................................................................. 87 Methods................................................................................................................. 87 Results ................................................................................................................... 92 Discussion ............................................................................................................. 94 Conclusion ............................................................................................................ 95 V. NEMATODE LIFE HISTORY TRAITS AND 18S rRNA COPY NUMBER .....................................................................108 Abstract ................................................................................................................108 Introduction ..........................................................................................................109 Objectives ............................................................................................................112 Methods................................................................................................................112 Results ..................................................................................................................118 Discussion ............................................................................................................121 Conclusion ...........................................................................................................124 VI. EPILOGUE ..........................................................................................................140 Summary ..............................................................................................................140 Implications..........................................................................................................142 Future Research ...................................................................................................142 v APPENDIX A: SUPPLEMENTAL METHODS ........................................................................144 Chapter III Supplemental Methods ..................................................................................144 Chapter V Supplemental Methods ...................................................................................146 APPENDIX B: SUPPLEMENTAL FIGURE AND GRAPHS ...................................................157 Chapter III Supplemental Figures and Graphs .................................................................157 Chapter V Supplemental Figures and Graphs ..................................................................163 REFERENCES ............................................................................................................................167 vi LIST OF FIGURES Figure Page 1.1 rRNA Structure across Organisms ................................................................................19 1.2 Tree of Life ...................................................................................................................20 2.1 Major Taxonomic Comparisons ...................................................................................37 2.2 Autocorrelation of 18S Sequence and Copy Number ...................................................38 2.3 Semi-variance of 18S Sequence and Copy Number .....................................................39 2.4 Cumulative Distribution Function ................................................................................40 2.5 Firmicutes Copy Number Tree .....................................................................................41 2.6 Example of Significant Phylogenetic Signal ................................................................42 2.7 Example of Non-significant Phylogenetic Signal .........................................................43 2.8 Silva Archaea Copy Number Tree ................................................................................44 2.9 Ancestral State