Community phylogenetics: methodological approaches and patterns in subarctic freshwater insect systems by Elizabeth E. Boyle A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Integrative Biology Guelph, Ontario, Canada © Elizabeth E. Boyle, September, 2012 ABSRTACT Community phylogenetics: methodological approaches and patterns in subarctic freshwater insect systems Elizabeth E. Boyle Advisor: University of Guelph, 2012 Dr. Sarah J. Adamowicz I aimed to expand our understanding of community assembly and species co-existence by examining the implications of phylogenetic robustness on metrics describing phylogenetic community structure, as well as the phylogenetic patterns of co-occurring insect species in Churchill, MB. Using a variety of tree reconstruction methods, I found that cytochrome c oxidase subunit I (COI) was able to accurately estimate phylogenetic community structure metrics calculated from a multi-gene phylogeny when using more biologically realistic approaches. This included incorporating known phylogenetic relationships among families, and methods that employ best-fit models of molecular evolution (i.e. Bayesian inference). My second study examined the phylogenetic community patterns of freshwater insects. Overall communities were phylogenetically clustered suggesting environmental filtering, but community structure varied with time, habitat, taxonomic group, and water chemistry (particularly pH and turbidity). My thesis has suggested more robust techniques for calculating phylogenetic community structure, and described patterns of phylogenetic community composition in subarctic freshwater insects. Acknowledgements First and foremost, I would like to thank my advisor Dr. Sarah Adamowicz. I am exceedingly grateful for the attention and time that you always gave me and my project. Your guidance, support, enthusiasm, insight, and inquisitiveness kept me motivated and improved my research. Thank you for giving me this opportunity, and all the help along the way. There are also numerous agencies that I am grateful for providing funding for my thesis work. I would like to thank Natural Sciences and Engineering Research Council of Canada (NSERC), International Barcode of Life (iBOL), Genome Canada, Ontario Genomics Institute, Canadian Foundation for Innovation, Ontario Ministry of Research and Innovation for providing funding for my molecular work. In addition, I am grateful for the support of the staff at the Canadian Centre for DNA Barcoding (CCDB) who helped me produce my sequences. I would also like to thank NSERC, the Churchill Northern Studies Centre, and Aboriginal Affairs and Northern Development Canada for their financial support for my field work. I am also very grateful to Dr. Karl Cottenie and Dr. Jinzhong Fu for their input into this project, and helping out with ‘cans of worms’. I would also like to thank Dr. Xin Zhou, Dr. David Ruiter, Dr. Jeffrey M. Webb, and Dr. Thomas S. Woodcock for their taxonomic expertise and their enthusiasm. A special thanks also needs to be given to my fellow graduate students. First, I would like to thank Amanda Winegardner for her assistance with the water chemistry readings and her help in the field. Thank you to my field mates that not only helped with collecting, but made sure I wasn’t eaten by a polar bear while I had my head in a bucket looking for insects. I am also grateful to Christina Carr and Claudia Bertrand for their molecular expertise and patience answering all of my questions. I would like to thank all of the members of the Adamowicz, Hebert, Gregory, Crease, Hajibabaei, and Smith labs for the laughs and good times. Finally, I would like to thank my family for all of their support and love throughout this entire process. iii Table of Contents Abstract .......................................................................................................................................... ii Acknowledgements ...................................................................................................................... iii List of Tables ............................................................................................................................... vii List of Figures ............................................................................................................................... ix Chapter 1: General introduction to phylogenetic community assembly ..................................1 Community assembly ...................................................................................................................1 Phylogenetic community approaches ...........................................................................................2 The utility of DNA barcoding ......................................................................................................5 Freshwater insects of Churchill, MB, Canada ..............................................................................6 Objectives of my thesis ................................................................................................................8 Chapter 2: Assessing the impact of phylogenetic reconstruction method upon measures of phylogenetic community structure .............................................................................................11 Abstract ......................................................................................................................................11 Introduction ................................................................................................................................11 Methods ......................................................................................................................................17 Field collection .......................................................................................................................17 Molecular analysis .................................................................................................................18 Phylogeny construction ..........................................................................................................19 Congruence of distance matrices ...........................................................................................20 Phylogenetic signal metrics ....................................................................................................21 Phylogenetic community structure metrics ............................................................................22 Results ........................................................................................................................................22 Phylogeny support ..................................................................................................................23 Distance matrix similarity ......................................................................................................23 Presence of phylogenetic signal .............................................................................................24 iv Estimation of phylogenetic community structure metrics ......................................................24 Discussion ..................................................................................................................................25 Discrepancy of metrics measuring phylogenetic signal .........................................................25 Best approaches for estimating phylogenetic community structure .......................................26 Utility of COI ..........................................................................................................................27 Conclusions ............................................................................................................................28 Chapter 3: Variation with habitat and time of phylogenetic structure in freshwater invertebrate communities of Churchill, MB, Canada ..............................................................39 Abstract ......................................................................................................................................39 Introduction ................................................................................................................................39 Methods ......................................................................................................................................43 Field collection .......................................................................................................................43 Molecular analysis .................................................................................................................43 Phylogeny construction ..........................................................................................................44 Phylogenetic signal in morphological traits ..........................................................................46 Phylogenetic community structure metrics ............................................................................46 Statistical analysis ..................................................................................................................46 Results ........................................................................................................................................47 Phylogenies.............................................................................................................................48