ENVIRONMENTAL VARIATION AND ITS EFFECT ON THE SUCCESS OF CROP- WILD HYBRIDIZATION IN THE RAPHANUS SPECIES COMPLEX by Kruti Shukla M.Sc, University of Guelph, 2013 B.Sc, University of Guelph, 2009 A dissertation presented to Ryerson University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the program of Molecular Science Toronto, Ontario, Canada, 2019 © Kruti Shukla, 2019 AUTHOR’S DECLARATION FOR ELECTRONIC SUBMISSION OF A DISSERTATION I hereby declare that I am the sole author of this dissertation. This is a true copy of the dissertation, including any required final revisions, as accepted by my examiners. I authorize Ryerson University to lend this dissertation to other institutions or individuals for the purpose of scholarly research. I further authorize Ryerson University to reproduce this dissertation by photocopying or by other means, in total or in part, at the request of other institutions or individuals for the purpose of scholarly research. I understand that my dissertation may be made electronically available to the public. ii Abstract ENVIRONMENTAL VARIATION AND ITS EFFECT ON THE SUCCESS OF CROP- WILD HYBRIDIZATION IN THE RAPHANUS SPECIES COMPLEX Kruti Shukla, Doctor of Philosophy, 2019 Molecular Science, Ryerson University Hybridization has been suggested as mechanism that can contribute to adaptive evolution and the success of crop-wild hybrid populations; but this response appears to depend upon environmental context. I explore how environmental variation affects crop trait expression, the strength and direction of selection on crop traits in radish weed populations, and the influence environmental variation has on crop-trait introgression across agricultural landscapes. Using the Raphanus crop-wild complex as a model system to study the environmental sensitivity of crop gene flow into weed populations, I first planted advanced-generation wild and crop-wild hybrid radish plants (that had previously evolved for three generations under relatively dry, relatively wet, or ambient control soil moisture or water-evolved conditions) into sheltered common gardens that were watered with low, ambient, or high soil moisture. From this work, hybridization and watering history did not enhance the success of advanced-generation hybrid plants relative to wild progenitors in Ontario, Canada. Next, I explored how phenotypic plasticity in response to environmental variation may distort a commonly used metric to measure the rate of evolution, the haldane. To determine the extent that plasticity affected estimates of evolutionary rate, I compared haldane estimates of advanced-generation water-evolved plants grown in a common garden that did not involve manipulation of ambient watering conditions. Estimates of the magnitude and direction of contemporary evolution differed significantly due to annual environmental variation, particularly for wild populations. Thus, I propose changes to the iii use of these equations and changes to the equation itself to help avoid generating false estimates of evolutionary rates. Finally, a meta-analysis of radish phenology and fecundity data collected from the last twelve years across four locations revealed that geography can affect the strength and direction of selection on crop- derived traits in weedy radish populations. This large, integrated study offers environmental risk assessment a new perspective on the role of environmental change on the success of crop-wild hybridization and its ability to generate weedy species. In summary, I provide evidence that environmental variation should be considered before making predictions about a crop trait’s evolutionary trajectory and persistence in a weedy plant population. iv Acknowledgements First, I would like to thank my advisor Lesley G. Campbell for all her unwavering support during this crazy ride. Her enthusiasm, guidance, and mentorship has been a motivating force during this PhD. Through our day-to-day interactions over the past four years we have both evolved (ha!) and grown as people and I am appreciative of the opportunity you have given me - thank you from the bottom of my heart. Thank you to my advisory committee members: Drs. Hafiz Maherali, Michael Arts, and Stephanie Melles and co-author Andrew Laursen for your advice, guidance, and sincerity. Thank you to my parents (Piyush and Toral Shukla) and my brother and his family for emotionally supporting me on this whirlwind of an adventure. I appreciate the encouragement and constant reinforcement you provided every single day and making sure I was taken care of. To Sudir, you have been an unconditional, loving support. Thank you for that you do and all that you have done. You keep me fed and happy and I love you. More importantly, you make a wonderful research assistant. Thank you for all your help with experimental set-up, data collection, data entry, emotional breakdowns, everything – you’re an honorary scientist in my book! I am grateful to all the amazing friends that have kept me going. First and foremost, Tarn Preet Parmar – we met as co-lab mates and grew to become amazing friends. We’ve gone through this wild journey together and I appreciate all your help. Our late nights at the lab collecting/analyzing data, our research talks, and technical support (obviously!) have gotten me through some intense times and I could not have done this without you. To my friends Lisa Huynh, Priscilla Sreedharan, and Nancy Lay thank you for your continuous love and dedication. I appreciate the rant sessions to the beer, dinners, and more beer – love you all. To Laruen Des Marteaux and Aurora Patchett even though you’re far away, it never felt that way. You were always there when I needed advice or a voice of reason. You have helped me through some difficult moments and am grateful to have you both in my life. Finally, thank you to all the amazing students that have helped me during my four years. v Contribution of Authors and Chapter Acknowledgements Chapter 2 Contributing Authors: K. Shukla (KS), Lesley G. Campbell (LGC), Andrew E. Laursen (AEL), Hafiz Maherali (HM), Jessica Benevides (JB), Neda Ejbari (NE). I appreciate the many students, too numerous to name, assisted in population maintenance and data collection between 2010-2016. The staff of the University of Toronto’s Koffler Scientific Research provided logistical support. The authors gratefully acknowledge the funding support from the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grants program (no. 402305-2011 to LGC), Ontario Graduate Scholarship (OGS), Queen Elizabeth II Graduate Scholarship (QEII), and the Faculty of Science Ryerson University (for a research fellowship to KS). KS wrote the manuscript and ran the data analysis with support from LGC, HM, and AEL. KS, JB, and NE helped with experimental setup, data collection, and data analysis. Chapter 3 Contributing Authors: K. Shukla (KS), Lesley G. Campbell (LGC), Hafiz Maherali (HM), Andrew E. Laursen (AEL), Jessica Benevides (JB), and Serena Sbrizzi (SS). We particularly appreciate insights of A. Snow, K. Mercer, and A. Weis in the development of this study and thankful to M.T. Arts and S. Melles for helpful edits to the MS. Many students, too numerous to name, assisted in population maintenance and data collection between 2010-2016. The staff of the University of Toronto’s Koffler Scientific Research provided logistical support. The authors gratefully acknowledge the funding support from the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grants program (no. 402305-2011 to LGC), Ontario Graduate Scholarship (OGS), Queen Elizabeth II Graduate Scholarship (QEII), and the Faculty of Science Ryerson University (for a research fellowship to KS). KS wrote the manuscript and ran the data analysis with support from LGC, HM, and AEL. KS, JB, and SS helped with experimental setup, data collection, and data analysis. vi Chapter 4 Contributing Authors: K. Shukla (KS), Lesley G. Campbell (LGC), Steve Hovick (SH), Shion Song (SS), Zachary Teitel (ZT). We particularly appreciate insights of A. Snow, K. Whitney, and R. Baucom in the development of this study. Many student researchers, too numerous to name, assisted in data collection in MI, ON, OH, and TX. The staff of the University of Michigan Biological Station, Koffler Scientific Reserve in Ontario, Canada, and Ohio State University Waterman Farm. Koffler Field Station and Ecological Reserves provided incredible field support. Funding was provided by NSERC Discovery (no. 402305-2011 to LGC). KS wrote the manuscript and ran the data analysis with support from LGC and SH. KS, LGC, SH, SS, and ZT helped with data collection and analysis. vii Table of Contents Abstract ......................................................................................................................................... iii Acknowledgements ....................................................................................................................... v Contribution of Authors and Chapter Acknowledgements ..................................................... vi Table of Contents ....................................................................................................................... viii List of Tables ................................................................................................................................ xi List of Figures ............................................................................................................................