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The Use of Regional Phylogenies in Exploring the Structure of Plant Assemblages

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The use of regional phylogenies in exploring the structure of plant assemblages Tammy L. Elliott Doctor of Philosophy Department of Biology McGill University Montr´eal, Qu´ebec, Canada 2015-09-015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Doctor of Philosophy c Copyright Tammy L. Elliott, 2015 All rights reserved Dedication I dedicate this thesis to my parents, who sadly both left this world much to early. I like to dream that you are both enjoying your time together in a place with no worries, where you can enjoy all of the wonderful things in life. Dad—Although you left us when we were so young, I daily cherish the special times the two of us spent together. The memories of exploring the countryside, visiting neighbours, caring for the pigs and skipping school to fish are always close to my heart. Mom—I miss your strength, interesting perspective (albeit humorously pessimistic), no-nonsense attitude towards life and listening ear. I hope that you are finding ways to enjoy your grandchildren and tend your beautiful gardens. I would like to assure you that yes—one day I will have a full-time job. If Roses grow in Heaven Lord, please pick a bunch for me. Place them in my Mother’s arms and tell her they’re from me. Tell her that I love her and miss her, and when she turns to smile, place a kiss upon her cheek and hold her for awhile Because remembering her is easy, I do it every day, but there’s an ache within my heart that will never go away. Author Unknown Acknowledgements This thesis is the result of the input of several different people to whom I am grateful. First, I would like to thank my supervisor, Jonathan Davies, for accepting me into his lab. I feel that he has offered the right amount of guidance over the last few years, allowing me to grow by making my own decisions. Second, I would like to thank my Supervisory Committee members—Sylvie de Blois and Catherine Potvin for providing advice on experimental design, analytical methods and overall thesis direction and structure. In addition, I thank Martin Lechowicz and Marcia Waterway for their help during the early stages of my doctoral studies, as well as Pierre Legendre and Guillaume Larocque for their assistance with statistical methods. Many thanks are extended to my labmates for the support and camaraderie they have offered in and outside of the office over the last few years. In particular, I thank Eraclis Araclides, Chelsea Chisholm, Ria Ghai, Jean-Phillipe Lessard, Ignacio Morales-Castilla, Will Pearse and Stephanie Shooner for reviewing and offering comments on my work. Additional thanks are offered to Eraclis Araclides, Frederic Boivin, Maxwell Farrell and Will Pearse for helping with my analyses, as well as Michael Becker for his awesome filmmaking abilities. I also thank Malie Lessard-Therrien for sharing her data. I acknowledge the perseverance of Liam Harris, Genevi`eve Lajoie and Kyle Martins for enduring the black flies and long work days in Schefferville. My gratitude is offered to Peter White for originally creating the Mnt. Irony sampling grid and to Oksana Choulik, Neil Ednie and the McGill Subarctic Research Station for providing logistical support while in the Schefferville area. I thank David Maneli and Stephanie Shooner for their help in the field at Mont St. Hilaire, as well as Robin Beaus´ejour, M´elanie Lapointe, Arold Lavoie and Catherine Polcz for helping to locate additional species on the ‘mountain’. This research would not be possible without the support of the McGill Herbarium and the Marie-Victorin Herbarium. Thanks are offered to Nadia Cavallin for her help and iii support in the field, herbarium and outside of work. I am very grateful for the advice of Geoffrey Hall, whose knowledge of the local flora improved my collection efforts at Mont St. Hilaire and led to many stimulating botanical conversations. In addition, I thank Kyle Martins and Marcia Waterway for their help at the McGill Herbarium. I also thank Kathryn Flinn, Rapha¨elle Fr´echon and countless volunteers for their help preparing my hundreds of herbarium specimens. My appreciation is also extended to George Argus, Paul Catling, Jim Phipps, Anton Reznicek and Jeff Saarela for kindly offering their plant identification services. I thank the African Centre for DNA Barcoding research for processing my DNA sam- ples. In particular, I thank Olivier Maurin and Michelle Van der Bank for responding to my countless e-mail messages and for ensuring that all samples were correctly processed. My gratitude is extended to the several funding agencies whose financial support allowed me to pursue my research interests. Specifically, I thank the Garfield Weston Foundation, the Natural Sciences and Engineering Research Council of Canada (NSERC), the Qu´ebec Centre for Biodiversity Science (QCBS) and McGill University for their generous scholarships. In addition, I thank the Canadian Polar Commission for logistical support in the field in the form of Northern Scientific Training Program (NSTP) grants. Additional thanks are offered to the many anonymous reviewers who have provided valuable comments on the manuscripts included within this thesis. I am also grateful for the help of other researchers for providing comments on my work. In particular, I thank Frieda Beaugrand, Heather Collins, Barnabas Daru, Vincent Fug`ere, Kiyoko Gotanda, Pascal Kropf, Patrick McCamphill, S´ebastien Portalier and Melissa Ward for their reviews. Finally, I thank my family for standing by my side as I have embarked on this multi- year challenging adventure. iv Abstract Unravelling the complexities of biological communities has long interested community ecologists. Molecular, computational and conceptual advances in the last fifteen years have led to the increasing incorporation of phylogenetic information into ecological anal- yses, creating a new field of ‘community phylogenetics’. Although the field of community phylogenetics has improved our understanding of the processes determining community composition, more recently the field has been challenged because of its reliance on several critical assumptions. In this thesis, I address some of these critiques by exploring novel empirical and analytical approaches. In Chapter 2, I describe the major challenges to sampling a comprehensive species pool, essential for generating regional phylogenies and testing community assembly mechanisms. I use a case study based on my work at Mont St. Hilaire, Qu´ebec to illustrate these challenges, and I make several recommendations for sampling that can be used by other researchers pursuing similar efforts in the future. I switch focus from regional species pools to plant communities in Chapters 3 and 4, where I combine co-occurrence and phylogenetic data on sedges (i.e. plants of the Cyperaceae family) near Schefferville, Qu´ebec to address assumptions related to species coexistence. I use an individual-based focal sampling approach in Chapter 3 to show that the phyloge- netic neighbourhood of a plant varies with the clade membership of the species, addressing the critique that it is individuals of a species and not communities that are ‘filtered’ by environment. I explore the assumption that competitive exclusion is most probable between closely related species in Chapter 4 by examining whether specialists are better competitors than generalists. My results suggest that niche width differences translate into differences in competitive abilities and that co-occurrence is more likely between distantly related species with differing niche widths, adding further insights into the relationship between phylogenetic relatedness and competitive abilities. Finally, in Chapter 5 I eval- uate the effectiveness of phylogenetic beta diversity methods for delineating ecological v boundaries. Previous work has focused on regional and global scales, whereas similar methods might not be as effective at differentiating local scale patches. As I demonstrate in this thesis, the field of community phylogenetics will remain relevant for unravelling the complexities of biological communities by using novel approaches. vi R´esum´e D´emˆeler la complexit´e des communaut´es biologiques a depuis longtemps int´eress´eles ´ecologistes des communaut´es. Les avanc´ees en biologie mol´eculaire, en informatique et les progr`es conceptuels durant les quinze derni`eres ann´ees ont conduita ` l’int´egration croissante de l’information phylog´en´etique dans les analyses ´ecologiques, cr´eant le nouveau champ de la phylog´enie des communaut´es. Bien que le domaine de la phylog´enie des communaut´es ait am´elior´e notre compr´ehension des processus qui d´eterminent la composition des communaut´es, plus r´ecemment, ce domaine a ´et´e contest´eenraisonde sa d´ependance `al’´egard de plusieurs hypoth`eses critiques. Dans cette th`ese, je r´eponds `a plusieurs de ces critiques en explorant de nouvelles approches empiriques et analytiques. Dans le chapitre 2, je d´ecris les principaux obstaclesal’´ ` echantillonnage d’un groupe com- plet d’esp`eces, essentiel pour g´en´erer des phylog´enies r´egionales et tester les m´ecanismes d’assemblage de la communaut´e. J’utilise une ´etude de cas bas´ee sur mon travail `a Mont-Saint-Hilaire, au Qu´ebec, pour illustrer ces probl`emes, et je fais plusieurs recom- mandations pour l’´echantillonnage qui peuvent ˆetre utilis´ees par d’autres chercheurs qui poursuivront des efforts similaires dans l’avenir. Je passe ensuite des groupes r´egionaux d’esp`eces aux communaut´es v´eg´etales dans les chapitres 3 et 4, o`u je combine des donn´ees de cooccurrence et de phylog´enie sur les plantes de la famille des Cyp´erac´ees pr`es de Schefferville, au Qu´ebec, pour r´epondre aux hypoth`eses relatives `a la coexistence des esp`eces. J’utilise une m´ethode d’´echantillonnage focal bas´e sur l’individu dans le chapitre 3 pour montrer que la proximit´ephylog´en´etique d’une plante varie avec la composition de clade de l’esp`ece, r´epondant `a la critique que ce sont les individus d’une esp`ece et non pas les communaut´es qui sont filtr´es dans les communaut´es.
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