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Assessing the Population Genetic Structure of the Endangered Cucumber Tree (Magnolia Acuminata) in Southwestern Ontario Using Nuclear and Chloroplast Genetic Markers

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Assessing the Population Genetic Structure of the Endangered Cucumber Tree (Magnolia Acuminata) in Southwestern Ontario Using Nuclear and Chloroplast Genetic Markers ASSESSING THE POPULATION GENETIC STRUCTURE OF THE ENDANGERED CUCUMBER TREE (MAGNOLIA ACUMINATA) IN SOUTHWESTERN ONTARIO USING NUCLEAR AND CHLOROPLAST GENETIC MARKERS. A Thesis Submitted to the Committee on Graduate Studies in Partial Fulfillment to the Requirements for the Degree of Master of Science in the Faculty of Arts and Science Trent University Peterborough, Ontario, Canada © Copyright by Cara E. Budd 2014 Environmental and Life Sciences M.Sc. Graduate Program September 2014 Assessing the population genetic structure of the endangered Cucumber tree (Magnolia acuminata) in southwestern Ontario using nuclear and chloroplast genetic markers. Cara E. Budd ABSTRACT Magnolia acuminata (Cucumber tree) is the only native Magnolia in Canada, where it is both federally and provincially listed as endangered. Magnolia acuminata in Canada can be found inhabiting pockets of Carolinian forest within Norfolk and Niagara regions of southwestern Ontario. Using a combination of nuclear and chloroplast markers, this study assessed the genetic diversity and differentiation of M. acuminata in Canada, compared to samples from the core distribution of this species across the United States. Analyses revealed evidence of barriers to dispersal and gene flow among Ontario populations, although genetic diversity remains high and is in fact comparable to levels of diversity estimated across the much broader range of M. acuminata in the USA. When examining temporal differences in genetic diversity, our study found that seedlings were far fewer than mature trees in Ontario, and in one site in particular, diversity was lower in seedlings than that of the adult trees. This study raises concern regarding the future viability of M. acuminata in Ontario, and conservation managers should factor in the need to maintain genetic diversity in young trees for the long-term sustainability of M. acuminata in Ontario. Key words: conservation genetics, population genetic structure, endangered, Magnolia acuminata, Carolinian, habitat fragmentation, microsatellites, cpDNA, genetic diversity, genetic differentiation II ACKNOWLEDGEMENTS First and foremost, I am undoubtedly extremely lucky to have parents whom have worked their whole lives to provide me with a life full of opportunity. If it wasn’t for their love, patience, and unlimited support, both emotionally and financially, I would not be half the person I am today. There are no words that could describe how grateful I am to have them, and I dedicate this project to them. I would like to express my sincerest gratitude to my project supervisor, Dr. Joanna Freeland, for her patience, enthusiasm, and optimism from beginning to end. Even at what seemed to be the most trying times, she always managed to stay positive and see the light at the end of the tunnel. Thank you for the constant reminder that everything will not go as planned and that it’s okay… do no stress, accept the situation and adapt to it. In addition, a big thanks to Dr. Marcel Dorken and Bill Crins for their willingness to participate in my supervisory committee, as well as their invaluable guidance and expertise regarding plant genetics and evolutionary biology. Thank you for taking the time out of your busy schedules to provide me with the support I needed at all levels of this project. I’d like to thank Graham Buck and Donald Kirk of the Ministry of Natural Resources for getting the ball rolling on this project. Without their instrumental assistance I would not have been able to acquire the necessary permission to collect samples from private landowners, nor have all the essential documents and background knowledge regarding the location and ecology of these beautiful trees. I must also acknowledge Danny Bernard of Big Creek Conservation Authority for providing me with the opportunity to visit and sample trees within the National Wildlife Area, as well as his vast knowledge regarding the natural heritage and history of the Long Point region. It was a truly an amazing and fun-filled research experience, and one I hope to have again. I cannot forget to thank Elizabeth Zimmer and Gabe Johnson at the Smithsonian Institute, for generously providing the Magnolia acuminata leaves and associated information from across the United States, allowing for the conservative comparison of diversity between the two regions. III A special thanks to Jennifer Paul for her help, accompaniment, and many laughs in the field and lab. To Marco Raponi, the genius behind my sampling equipment! Thank you for the drives, coffee runs, and what seemed to be regular “therapy” sessions. I really couldn’t have asked for a better friend to have taking this MSc. journey with me. Adam Wilford, thank you for being so tall and most importantly, my easy-going better half. Without you I wouldn’t have the leaves to complete this project nor hair on my head. It means the world to me that I was able to share this project, experience and the love of Ontario’s southwest with you. To all those whom I failed to mention, your contributions have in no way gone unnoticed and I appreciate all you have done to make this project possible. IV TABLE OF CONTENTS ABSTRACT II ACKNOWLEDGEMENTS III-IV LIST OF FIGURES VI LIST OF TABLES VII GENERAL INTRODUCTION 1 INTRODUCTION 8 METHODS 21 RESULTS 32 DISCUSSION 43 REFERENCES 68 APPENDICIES 86 APPENDIX I- DISTRIBUTION AND NUMBER OF SAMPLED MAGNOLIA ACUMINATA ACROSS ONTARIO AND UNITED STATES 86 APPENDIX II- MAP OF THE DISTRIBUTION OF UNITED STATES MAGNOLIA ACUMINATA SAMPLES 87 APPENDIX III- RAW GENOTYPIC DATA: III-A. ONTARIO MAGNOLIA ACUMINATA 88-96 III-B. UNITED STATES MAGNOLIA ACUMINATA 97-99 APPENDIX IV- CONSERVATIVE COMPARISONS OF ALLELIC DIVERSITY BETWEEN: III-A. ONTARIO AND THE UNITED STATES 100-101 III-B. NORFOLK COUNTY AND THE MUNICIPALITY OF NIAGARA 102-103 III-C. NORFOLK COUNTY AND THE UNITED STATES 104-105 III-D. MUNICIPALITY OF NIAGARA AND THE UNITED STATES 106-107 APPENDIX V- CLUSTER ASSIGNMENT VALUES: IV-A. STRUCTURE POPULATION CLUSTER ASSIGNMENT 108 IV-B. STRUCTURE INDIVIDUAL CLUSTER ASSIGNMENT 109-113 IV-C. TESS POPULATION CLUSTER ASSIGNMENT 114 IV-D. TESS INDIVIDUAL CLUSTER ASSIGNMENT 115-119 V LIST OF FIGURES FIGURE 1: DISTRIBUTION OF COLLECTED M. ACUMINATA SAMPLES FROM NATURAL STANDS WITHIN ONTARIO AND THE UNITED STATES. 22 FIGURE 2: ∆K RESULTS BASED ON STRUCTURE ANALYSIS. ∆K CALCULATED BY STRUCTURE HARVESTER AND ACCORDING TO EVANNO ET AL. (2005) FOR K VALUES RANGING FROM 1 TO 8. 37 FIGURE 3: TESS CLUSTERING ANALYSIS OF M. ACUMINATA SAMPLED ACROSS 12 SITES IN ONTARIO. CLUSTERING WAS COMPLETED USING (A) CAR AND (B) BYM MODELS FOR K VALUES RANGING FROM 2 TO 10. 38 FIGURE 4: DISTRIBUTION OF M. ACUMINATA CLUSTERS IN NORFOLK COUNTY BASED ON CLUSTER ANALYSIS RESULTS. 39 FIGURE 5: DISTRIBUTION OF M.ACUMINATA CLUSTERS IN THE MUNICIPALITY OF NIAGARA BASED ON CLUSTER ANALYSIS RESULTS. 40 FIGURE 6: POSTERIOR ESTIMATES OF ASSIGNMENT PROBABILITIES FOR (A) STRUCTURE AND (B) TESS BYM MODEL, WHERE KMAX= 7. SITE AND ASSOCIATED CLUSTER NUMBERS ARE DEFINED IN TABLE 7. 41 VI LIST OF TABLES TABLE 1: NUCLEAR MICROSATELLITE PRIMERS USED TO ASSESS THE POPULATION GENETIC STRUCTURE OF M. ACUMINATA IN ONTARIO AND THE UNITED STATES. 23 TABLE 2: CHLOROPLAST MINISATELLITE REGIONS FOR WHICH AMPLIFICATION PRIMERS WERE DESIGNED. 25 TABLE 3: GENETIC VARIABILITY OF FIVE MICROSATELLITE LOCI AVERAGED ACROSS ALL LOCI AND POPULATIONS OF M. ACUMINATA USING GENOTYPIC AND PHENOTYPIC DATA. 34 TABLE 4: SUMMARY OF GLOBAL F STATISTICS (FST) AND JOST D (D_EST) AMONG THE 7 IDENTIFIED CLUSTERS IN ONTARIO (K=7), NORFOLK COUNTY (K=5), AND THE MUNICIPALITY OF NIAGARA (K=2). 35 TABLE 5: ANALYSIS OF MOLECULAR VARIANCE CALCULATED USING PHENOTYPIC DATA FOR ONTARIO, NORFOLK COUNTY, AND THE MUNICIPALITY OF NIAGARA. 36 TABLE 6: PAIRWISE FST AND D_EST BETWEEN THE INFERRED CLUSTERS OF M. ACUMINATA IN ONTARIO. 36 TABLE 7: ONTARIO M. ACUMINATA SAMPLE SITES AS DEFINED BY GEOGRAPHIC LOCATION AND CLUSTER. CLUSTER ASSIGNMENTS BASED ON TESS BYM MODEL AND STRUCTURE RESULTS FOR K=7. 41 TABLE 8: ALLELE SIZES FOR ALL FIVE CHLOROPLAST REGIONS IDENTIFIED AMONG ALL INDIVIDUALS FROM ONTARIO AND US POPULATIONS OF MAGNOLIA ACUMINATA. 42 TABLE 9: GENETIC DIVERSITY OF CANOPY TREES AND SEEDLINGS OF ONTARIO M. ACUMINATA USING GENOTYPIC AND PHENOTYPIC DATA FROM FIVE MICROSATELLITE LOCI. 42 TABLE 10: GENETIC DIVERSITY OF CANOPY TREES AND SEEDLINGS OF ONTARIO M. ACUMINATA WITHIN SITES NWA AND FD USING GENOTYPIC AND PHENOTYPIC DATA. 43 VII 1 GENERAL INTRODUCTION Deciduous forest dominated North America during the latter part of the Mesozoic era (Braun, 1947). By the Eocene epoch, vegetation in the west had shifted in response to latitudinal climate shifts, resulting in the contraction of subtropical species and the expansion of those more temperate species found in the north, with dicot fossils from the Upper Cretaceous revealing the dominance of the broad-leaved forest across eastern North America. During this time, the Coastal Plain of the east and the Appalachian Highlands contained a large proportion of the existing genera of the contemporary deciduous forest (Braun, 1955) including one of the oldest genera of broad-leaved trees in North America, Magnolia (Magnoliaceae). While time of divergence among Magnolia spp. is not completely known, Magnolias were not only abundant but substantial diversification had occurred during the Miocene epoch when North America had a warm and humid, tropical climate (Goldenberg et al., 1990). Magnolia spp. were widely distributed, predominantly inhabiting riparian areas, extending southward from what is now the current latitude of Nunivak Island, Alaska (Flannery, 2003). While repeated stochastic environmental events altered much of the landscape, southern United States remained a haven for a variety of taxa, especially during the Wisconsinan glaciation when northern species sought refugia south of the Laurentian Ice Sheet (Braun 1955; Wright 1964; Waldron 1993; Flannery 2003). Among the many species which would have required southerly refugia due to the inhospitability of the Great Lakes Basin during full glaciation was the Cucumber tree (Magnolia acuminata), Canada’s only native Magnolia, which is 2 both federally and provincially listed as endangered (Species at Risk in Ontario, 2014).
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