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DNA Barcode Variability in Canadian Cnidaria by Kathryn Hotke a Thesis

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DNA Barcode Variability in Canadian Cnidaria by Kathryn Hotke a Thesis DNA Barcode Variability in Canadian Cnidaria By Kathryn Hotke A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Masters of Science in Integrative Biology Guelph, Ontario, Canada © Kathryn Hotke, September 2015 ABSTRACT DNA Barcode Variability in Canadian Cnidaria Kathryn Hotke Advisor: University of Guelph, 2015 Professor P.D.N. Hebert This thesis investigates patterns of sequence variation in Canadian Cnidaria for the DNA barcode region of the cytochrome c oxidase subunit 1 (COI) gene. As such, it begins development of a DNA barcode reference library for this phylum. This work confirms the COI gene region as an effective tool for delineating currently recognized species of cnidarians and revealing cryptic species. As well, this study shows the value of COI barcodes in the identification of newly collected specimens and morphologically unusable specimen fragments. A detailed analysis of the genus Cyanea explores the incidence of cryptic taxa, revealing high genetic diversity. The results from this study have implications for the utility of DNA barcoding both for documenting biodiversity and broadening our understanding of biogeographic patterns of Cnidaria. Acknowledgements Firstly, I would like to thank my advisor Dr. Paul Hebert for providing me with guidance and support during my program. You always encouraged me to travel to different collection sites across Canada and take advantage of all opportunities presented to me. I am also very grateful of your support of my choice to enter the Doctor of Veterinary Medicine program. I am also incredibly grateful for the input I received from my committee members, Dr. Elizabeth Boulding and Dr. Teresa Crease. Your enthusiasm for this project kept me motivated and your promptness with feedback and advice was always appreciated. I would like to thank the Natural Sciences and Engineering Research Council of Canada and the Ontario Ministry of Training, Colleges and Universities for funding this research. I am grateful to members of the Pacific Biological station including Dave Workman and Malcolm Wyeth for allowing me on their scientific cruise of Hecate Strait. I am thankful to Bill Austen for taking me on sample collection trips around the Gulf Islands. I would like to thank Jack Fife and the members of the St. Andrews Biological Station and Huntsman Marine Center for being so accommodating and allowing me to use their facilities. I am also very grateful to the Stephanie Gagnon and members of the Marine Environment Discovery Center for performing scientific dives, collecting specimens and providing me with accommodations during my field season. As well, I am thankful to Danny Kent and members of the BC Waters section for their behind- the-scene access of the Vancouver Aquarium. I would also like to thank Paula Romagosa from the Shaw Ocean Discovery Center, Jill Marvin from l’Aquarium du Quebec, Laurent Robichaud and Conrad Allen from l’Aquarium et Centre Marin du Nouveau-Brunswick and Jim Cornall from the Fundy Discovery Aquarium. I would also like to extend my gratitude to Dr. Elizabeth Boulding, Kara Layton, Luc Savoie from Department of Fisheries and Oceans (DFO) Moncton, Dave Hardie from the Bedford Institute of Oceanography, Jamie Emberly of the St. Andrews Biological Station, Philippe Sargent of DFO St. John, Diane Archambault of the Maurice Lamontagne Institute and Patrick Allaire for their help in specimen collections. iii Lastly, I would like to thank the Canadian Centre for DNA Barcoding (CCDB) and Sean Prosser for helping me without delay with PCR, sequence acquisition and interpreting my results. A sincere thank you to all graduate students in the Hebert, Adamowicz and Hajibabaei labs for providing input into my project and contributing greatly to my happiness during this program. I especially want to thank Monica Young for her advice, patience and willingness to help me out with whatever problems I encountered. Finally, I would like to thank my close friends and family, who provided me with love and support throughout this project. iv Table of Contents Abstract…………………………………………………………….………………………………………ii Acknowledgements………………….……………………………………………………………………iii Lists of Figures…………………….……………….……………………..…….…………………..……vii List of Tables……………………………………….……………….….………………………..………..ix General Introduction……………...………………………………………………………………………1 Chapter 1: Patterns of DNA Barcode Variation in Canadian Cnidarians…….…...….………………4 Abstract……………………………………………………………………………….…………………4 Introduction.…………………………………………………………………………..…………………5 Methods………………………………………………………………………………………………….7 Specimen Collection and Taxonomy ………………………………………………………………7 DNA Isolation, Extraction and Amplification…...…………………………………………………7 Species Delineation………………………..……………………………………………….…………9 Sequence Analysis…………………….........…………………………………………………………9 Results…………………………………………………………….……………………………………..9 Taxon Diversity………….………………………………………..……………………………....…9 Sequence Recovery…………………………………………………..…………………………....…10 Scyphozoa …………………………………….…………………………...…………………………11 Aurelia aurita…………………………………….…………………...…………………………12 Phacellophora camtschatica…………….……………………………………………………13 Hydrozoa ……………………………………….……………………………..………………………13 Sarsia…………………………………………..…………………………………………………14 Hydra…………………………………..………………………………………………...………14 Obelia………………………………….………………………………………………………...15 Staurozoa ………………………………..…………….….……………………………………………15 Anthozoa ……………………………………….……………………..………………………………16 Pachycerianthus……………………………….…………………...……………………………17 Gersemia………………………………………….………………………………………………17 Pennatula…………..…………………………………….…………..…………………………17 Anthopleura……………………………………………………………………….……………18 Urticina………………..…………………………………….…………………………………18 Stomphia……………..…………………………………….……………………..……………19 Discussion………………………………………………………………………………………...……19 Collection……………………………….…………………………………………………...…20 Sequencing Success in Cnidaria……….………………………………………..……………21 Patterns of Sequence Variation…….…………………………………………..……….……21 Low Interspecific Divergence in Anthozoa…………………………………….……………22 Urticina………………..…………….…………….………….……………………..……………24 Stomphia……………..…………………………………………………………...……..……25 Cases of Cryptic Species…….…………………………………………….………....………26 Conclusions……………………………………………………..………………...…………27 Chapter 2: Revealing Cryptic Diversity in the Scyphozoan Cyanea capillata………………….……58 Abstract……………………………………………………………………………………………...…58 Introduction.…………………………………………………………………………...……….....……59 Methods……………………………………..………………………………………………………….61 Specimen Collection and Taxonomy ……………………..………………………………………61 DNA Isolation, Extraction and Amplification…………….……………..…………..……………61 Species Delineation…………………………………………..………………..……………………63 Sequence Analysis…………………….........…………………..……………………………………64 Morphological Analysis……………………………………...……..………………………………65 Salinity Data……..…………………….........…………..……..…………………………….………65 v Results…………………………………………………………………………………………….…..66 Collections and Sequence Recovery……………..…..……………………………………………66 COI Phylogenetic Analysis…………………………………………………………………………66 Geographic Distribution and Collection..………………………………………..………………67 Distribution of Lineages Relative to Salinity…..…………………………………….……………67 16S, ITS1 & ITS2 Analysis………..…….………………………..……………………………...…68 Relationships between Canadian Cyanea and those from other Regions………………...………68 Discussion…………………………………………………………………………………………...…70 General Conclusions..………………………………………………………………..………..…………95 Literature Cited…….………………………………………………………………………………….…97 Appendix A: Chapter 2 Supplementary Material……..………………………......…………………110 Appendix B: Collection Data……………………………...………………………...…………………115 Appendix C: R Code….……………………………..………………………………….………………157 vi List of Figures Chapter 1..…………………………………………………………………………………………………4 Figure 1.1 Sampling locations and the number of specimens (indicated by the white numbers) examined in this study………………………………………………...…………………….…..……..28 Figure 1.2 Neighbor-joining tree of scyphozoan COI sequences…………………….…..…………...29 Figure 1.3 Fragmented and 95% EtOH dehydrated specimens identified by COI sequences…....…...30 Figure 1.4 Neighbor-joining tree of Canadian Aurelia aurita COI sequences……….....…………….31 Figure 1.5 Nearest neighbor barcode gap of Scyphozoa, Hydrozoa and Staurozoa COI sequences….32 Figure 1.6 Neighbor-joining tree of Canadian and GenBank Aurelia spp. COI sequences…………..33 Figure 1.7 Neighbor-joining tree of Canadian Phacellophora camtschatica COI sequences…...........34 Figure 1.8 Neighbor-joining tree analysis of hydrozoan COI sequences………………….……..…...35 Figure 1.9 Melicertum octocostatum specimens from BOLD: ACO2504……………………...……..36 Figure 1.10 Neighbor-joining tree of Canadian Sarsia COI sequences……………..…..…….....…....36 Figure 1.11 Neighbor-joining tree of Canadian Hydra COI sequences ………………....…......….….37 Figure 1.12 Neighbor-joining tree of Canadian Obelia COI sequences …………...…….....………...38 Figure 1.13 Neighbor-joining tree of Canadian staurozoan COI sequences………….....…......……...38 Figure 1.14 Neighbor-joining tree of anthozoan COI sequences…………………………...…………39 Figure 1.15 Neighbor-joining tree of Canadian Pachycerianthus COI sequences.……...…..…….….40 Figure 1.16 Nearest neighbor barcode gap of Anthozoa COI sequences…………………….…..…...41 Figure 1.17 Neighbor-joining tree of Canadian Gersemia COI sequences………………….…....…..42 Figure 1.18 Neighbor-joining tree of Canadian Pennatula COI sequences……………….…...……..43 Figure 1.19 Anthopleura species from BOLD: AAK0746…………………………………….……...44 Figure 1.20 Neighbor-joining tree of Canadian Anthopleura COI sequences………………...……....45 Figure
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