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UNIVERSITY of CALIFORNIA, MERCED Adapting in Times of Stress UNIVERSITY OF CALIFORNIA, MERCED Adapting in Times of Stress: Community Responses in Monkeyflowers, Microbes, and Classrooms A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Quantitative and Systems Biology by Jackie E. Shay Committee in Charge Professor David H. Ardell, Chair Professor A. Carolin Frank, Research Advisor Professor Jason P. Sexton, Research Advisor Professor Gordon M. Bennett Professor Clarissa J. Nobile Professor Brian A. Perry 2021 © Copyright Chapter 4 © 2020 Frontiers Media SA Chapter 5 © 2021 American Society for Microbiology All other chapters © 2021 Jackie E. Shay All rights reserved The Dissertation of Jackie E. Shay, is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ________________________________________________________________________ A. Carolin Frank Ph.D. Research Advisor ________________________________________________________________________ Jason P. Sexton Ph.D. Research Advisor ________________________________________________________________________ Gordon M. Bennett Ph.D. ________________________________________________________________________ Clarissa J. Nobile Ph.D. ________________________________________________________________________ Brian A. Perry Ph.D. ________________________________________________________________________ David H. Ardell Ph.D. Chair University of California, Merced 2021 iii To my family, friends, mentors, and students. o To my husband, Dave, for being an adventurous field partner, a steady rock, and a warm embrace. You got me here. o To my son, Marty, for pushing me after I pushed you. You are my reason. o To Heather, for igniting the fire in me. This is for you. o iv TABLE OF CONTENTS List of Figures ............................................................................................................................................... viii List of Tables .................................................................................................................................................. xi Acknowledgements........................................................................................................................................ xii Curriculum Vita ............................................................................................................................................ xiv Dissertation Abstract ........................................................................................................................................1 Chapter 1: Is the leading edge of a species range becoming a climate refuge?.........................................2 1.1. Abstract .......................................................................................................................................2 1.2. Introduction .................................................................................................................................2 1.3. Methods .......................................................................................................................................4 1.3.1. Study species and background ...................................................................................4 1.3.2. Climate garden experiment ........................................................................................4 1.3.3. Statistical analysis ......................................................................................................4 1.4. Results .........................................................................................................................................5 1.4.1. How does lifetime fitness vary across the range? ......................................................5 1.4.2. Is there evidence of climate adaptation, and if so, in what sense or population context? ................................................................................................................................5 1.4.3. Does spatial, genetic, or climate variation predict fitness across the species range? 6 1.5. Discussion ...................................................................................................................................6 1.5.1. Rear- and leading-edge adaptive responses ...............................................................6 1.5.2. Local adaptation and fitness variation at the edges of the species range ...................7 1.5.3. Climate predicts fitness variation only at the leading edge .......................................7 1.6. Conclusions and implications for climate change responses ......................................................8 1.7. Acknowledgments .......................................................................................................................8 1.8. References ...................................................................................................................................9 Chapter 2: Rules of plant species ranges: Applications for conservation strategies ..............................21 2.1. Abstract .....................................................................................................................................21 2.2. Introduction ...............................................................................................................................21 2.3. Are plant species range limits real? ...........................................................................................22 2.3.1. The essence of plant species ranges in a changing world ........................................22 2.3.2. Plant species ranges on the move.............................................................................22 2.3.3. Future directions ......................................................................................................23 2.4. Do biotic interactions influence patterns across species ranges? ..............................................24 2.4.1. Evidence of the importance of biological interactions on species ranges ...............24 2.4.2. Both positive and negative interactions matter ........................................................24 2.4.3. Future directions ......................................................................................................25 2.5. Do different regions of a species range hold predictable adaptive or resilient properties?.......26 2.5.1. The abundant center hypothesis is not a general rule ..............................................26 2.5.2. Genetic variation determines adaptive potential ......................................................27 2.5.3. Local adaptation follows adaptive potential ............................................................27 2.5.4. Future directions ......................................................................................................28 2.6. Are there predictable effects of gene flow on adaptation across species ranges? .....................28 2.6.1. Gene flow across species ranges ..............................................................................28 2.6.2. Isolation by distance is prevalent in plants ..............................................................29 2.6.3. Isolation by environment is also common in plants.................................................29 2.6.4. The myth of gene swamping in the creation of range limits....................................30 2.6.5. The potential of genetic rescue in conservation .......................................................30 2.6.6. Future directions ......................................................................................................31 2.7. Does range size predict vulnerability under global change? .....................................................31 2.7.1. Range size matters ...................................................................................................31 2.7.2. No range should be left behind in conservation.......................................................32 v 2.7.3. Future directions ......................................................................................................33 2.8. Conclusions ..............................................................................................................................34 2.9. Acknowledgments .....................................................................................................................34 2.10. References ...............................................................................................................................35 Chapter 3: Spatial, temporal, and environmental variation structures native monkeyflower endophytes .....................................................................................................................................................56 3.1. Abstract .....................................................................................................................................56 3.2. Introduction ...............................................................................................................................56 3.3. Methods .....................................................................................................................................57 3.3.1. Study system ............................................................................................................57 3.3.2. Experimental design and sampling ..........................................................................58
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