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(Physella Johnsoni) Using Pool-Seq University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2019-01-07 Conservation genomics of the endangered Banff Springs Snail (Physella johnsoni) using Pool-seq Stanford, Brenna Stanford, B. (2019). Conservation genomics of the endangered Banff Springs Snail (Physella johnsoni) using Pool-seq (Unpublished master's thesis). University of Calgary, Calgary, AB. http://hdl.handle.net/1880/109445 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Conservation genomics of the endangered Banff Springs Snail (Physella johnsoni) using Pool-seq by Brenna C.M. Stanford A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE GRADUATE PROGRAM IN BIOLOGICAL SCIENCES CALGARY, ALBERTA JANUARY 2019 © Brenna C.M. Stanford 2019 Abstract Understanding how species persist and adapt to local habitats is a fundamental question for species of conservation concern. Located in Banff National Park, the endangered snail, Physella johnsoni, inhabits seven highly specialized thermal springs. P. johnsoni undergo yearly population bottlenecks with minimal to no dispersal among springs. The consequences of these processes on genetic population structure are unknown. To investigate effects of habitat and life history on P. johnsoni’s genome and to test the hypothesis of a single panmictic population, I collected 20 to 40 snails/population for P. johnsoni and a closely related snail, P. gyrina, in adjacent, non-thermal water. Using whole genome pooled-sequencing, millions of single nucleotide polymorphisms were captured. These genetic variants resolved significant genetic divergence between P. johnsoni and P. gyrina. In addition, I detected distinct genetic clusters and reduced nucleotide diversity within each spring, indicative of strong micro-geographical population structure and suggestive of a role for genetic drift. These results suggest that P. johnsoni from each spring represent a distinct genetic unit, which has conservation implications for the designation of designatable unit status under COSEWIC, and where mixing of snails may reduce the consequences of genetic drift. ii Acknowledgments To my fantastic supervisor, Sean, I cannot begin to thank you enough for your guidance, patience, and humour. I am so excited for the opportunity to keep working with you. I am incredibly grateful for the wonderful group of people you have brought into this lab and for the environment that you foster. To Danielle, James, Jessy, Jori, Sara, Tegan, and Teresa, you are truly amazing. As scientists, leaders, and people I am so fortunate to call friends. Thank you for putting up with my distractions, tears and countless questions. Thank you for the many laughs, deep conservations, hugs and coffee. This work would not be anywhere close to this point without all of your scientific knowledge and support. To my committee members, Dwayne Lepitzki and Jana Vamosi – a huge thank you for everything you’ve done to support me in this work! A special thank you, Dwayne, for braving the cold, the snow and the heat and mosquitos, to make sure I not only lived through but thoroughly enjoyed my field season. To Parks Canada, specifically Mark Taylor, thank you so much for bringing me onto this project. It has been an absolute pleasure working with you. To my family, where do I even begin? Thank you for always believing in me, knowing when to step in, and when to let me find my own way. You challenge me, support me and make me laugh so hard. I will never be able to tell you how grateful I am for everything you’ve done and continue to do for me. And last but not least, thank you, Peter. You have been so incredibly understanding, supportive and I love you so very much. iii Table of Contents ACKNOWLEDGMENTS ........................................................................................................................ III TABLE OF CONTENTS .......................................................................................................................... IV LIST OF TABLES .................................................................................................................................... VI LIST OF FIGURES ................................................................................................................................. VII CHAPTER 1 GENERAL INTRODUCTION .......................................................................................... 1 1.1 INTRODUCTION .................................................................................................................................... 1 1.2 STUDY SYSTEM ................................................................................................................................... 8 1.3 OBJECTIVES ......................................................................................................................................... 9 CHAPTER 2 CONSERVATION GENOMICS IN THE BANFF SPRINGS SNAIL ........................ 13 2.1 INTRODUCTION .................................................................................................................................. 13 2.2 METHODS .......................................................................................................................................... 17 2.2.1 Sampling.....................................................................................................................................................17 2.2.2 DNA extraction ..........................................................................................................................................19 2.2.3 DNA quantification and quality check .......................................................................................................19 2.2.4 Constructing DNA pools for Pool-seq .......................................................................................................19 2.2.5 DNA sequencing ........................................................................................................................................20 2.2.6 Genomic analysis .......................................................................................................................................20 2.2.7 Pairwise FST ...............................................................................................................................................22 2.2.8 Nucleotide diversity ...................................................................................................................................22 2.3 RESULTS ............................................................................................................................................ 23 2.3.1 DNA extraction, quantification and quality ...............................................................................................23 2.3.2 DNA sequencing and pre-processing .........................................................................................................23 2.3.3 Pairwise FST ...............................................................................................................................................24 2.3.4 Nucleotide diversity ...................................................................................................................................24 2.4 DISCUSSION ....................................................................................................................................... 24 2.4.1 Population structure and nucleotide diversity between P. johnsoni and P. gyrina populations ................25 2.4.2 Population structure and nucleotide diversity within P. johnsoni and P. gyrina populations ...................27 2.4.3 Broader implications and conservation recommendations ........................................................................29 2.4.4 The utility of Pool-seq in conservation ......................................................................................................31 2.4.5 Caveats.......................................................................................................................................................33 2.4.6 Conclusions ................................................................................................................................................34 CHAPTER 3 GENERAL CONCLUSIONS .............................................................................................................41 iv REFERENCES ............................................................................................................................................................43 APPENDIX A: GENOMIC ANALYSIS PIPELINE ..............................................................................................55 APPENDIX B: DNA AND SEQUENCING QUALITY ..........................................................................................79 APPENDIX C: POPOOLATION2 PAIRWISE FST ESTIMATES .......................................................................82 v List of Tables Table 2.1 Number of SNPs within
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