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SFU Thesis Template Files Reconstructing Northern Fur Seal Population Diversity through Ancient and Modern DNA Data by Cara Leanne Halseth B.Sc., University of Northern British Columbia, 2011 Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Arts in the Department of Archaeology Faculty of Environment © Cara Leanne Halseth 2015 SIMON FRASER UNIVERSITY Summer 2015 Approval Name: Cara Leanne Halseth Degree: Master of Arts Title: Reconstructing Northern Fur Seal Population Diversity through Ancient and Modern DNA Data Examining Committee: Chair: Catherine D‟Andrea Professor Dongya Yang Senior Supervisor Professor Deborah C. Merrett Supervisor Adjunct Professor Iain McKechnie External Examiner SSHRC Postdoctoral Fellowship Dept of Anthropology University of Oregon Date Defended/Approved: July 2, 2015 ii Abstract Archaeological and historic evidence suggests that northern fur seal (Callorhinus ursinus) has undergone several population and distribution changes (including commercial sealing) potentially resulting in a loss of genetic diversity and population structure. This study analyzes 36 unpublished mtDNA sequences from archaeological sites 1900-150 BP along the Pacific Northwest Coast from Moss et al. (2006) as well as published data (primarily Pinsky et al. [2010]) to investigate this species‟ genetic diversity and population genetics in the past. The D-loop data shows high nucleotide and haplotype diversity, with continuity of two separate subdivisions (haplogroups) through time. Nucleotide mismatch analysis suggests population expansion in both ancient and modern data. AMOVA analysis (FST and ΦST) reveals some „structure‟ detectable between several archaeological sites. While the data reviewed here did not reveal dramatic patterning, the AMOVA analysis does identify several significant FST values, indicating some level of ancient population „structure‟, which deserves future study. Keywords: Northern fur seal; ancient DNA; genetic diversity; archaeology iii Acknowledgements There are many people to thank for supporting me in my graduate studies. First, I would like to thank my supervisory committee, Dr. Dongya Yang who was my senior supervisor and Dr. Deborah Merrett for their guidance throughout my time at Simon Fraser University. Without their support, completion of this thesis would not have been possible. Thank you for sticking by me through this sometimes winding journey, and for allowing me the freedom to explore this topic. I would also like to thank Dr. Iain McKechnie, my external examiner, for his helpful comments on my thesis. In addition, I would like to extend my sincerest gratitude for allowing me to use the sequence data from one of his studies for my thesis. In addition, even though I have never met them, I would like to also thank Dr. Madonna Moss, Dr. Seth Newsome, Dr. Camilla Speller, Dr. Alan McMillan, Dr. Robert Losey and Dr. Paul Koch, the remaining authors responsible for contributing the critical ancient DNA source data for this project. Without their work, this thesis would not have been possible. I would like to extend my gratitude to the SFU Ancient DNA lab group members who provided support throughout my studies here, particularly my colleague and fellow student Antonia Rodrigues, who also provided me with laboratory training and guidance throughout my project. Throughout my time at SFU I really enjoyed our lab meetings, the collaborative working environment, and the supportive team in the lab. The staff at Simon Fraser University, including Andrew Barton, Shannon Wood, Peter Locher, Merrill Farmer, Laura Walker, Jen Van Rassel and Chris Papaianni, aided me in a number of capacities over the course of my degree. I would also like to thank Dr. Dana Lepofsky for her support. The staff of the Archaeology Department are terrific and I would like to extend my appreciation to them as well. In addition, I would like to thank Catherine Louie from the SFU Library for her assistance with formatting this thesis. iv This thesis and my graduate studies work was funded by the Social Sciences and Humanities Research Council‟s Joseph-Armand Bombardier Canada Graduate Scholarship, Simon Fraser University‟s Provost‟s Prize of Distinction and Master‟s Graduate Fellowship, and by a handful of teaching assistant opportunities through the Department of Archaeology. A special thank you goes out to Dr. Brent Murray at the University of Northern British Columbia (UNBC) and Dr. Arne Mooers at Simon Fraser University. Your expertise and unselfishly offered advice on population genetics topics provided me with the guidance I needed to confidently move forward with my analysis. The faculty and staff at UNBC have always shown their support for me throughout my academic career. Even though I am no longer one of their own students, they took time during their busy schedules to provide thoughtful feedback on my thesis presentation and help prepare me for the defense that lay ahead. I would also like to thank Nikolaos Andreakis, a random stranger who, halfway across the world, took time out of his day to assist me with a critical data conversion issue. Most importantly, I could not have done any of this without the love and support of my family, and of an honorary member of my family, Laura Ryser. My parents and Laura provided assistance with the exacting and time-consuming task of editing and formatting the thesis, even though they had no idea what I was writing about. In what fortuitously turned out to be a mutually beneficial arrangement as he worked to meet the requirements of a cartography course, my brother Colin generated the maps used in this thesis. In addition, my family provided both emotional and financial support for my studies here at SFU, enduring long and frequent phone and Skype calls when I was lonely and ensuring I had the sustenance I needed to push forward by stocking up my fridge and freezer with groceries every time they came to town. My grandparents, Shirley and Ray Halseth, helped me acclimatize to the „big‟ city and gave me a home away from home, a place to have a fresh cooked meal, catch up on my laundry, and enjoy those holidays I spent in Vancouver. I also need to thank my grandmother, Ursula Sturhahn, for the wonderful care packages that she sent to me, my uncle Robert for all the long drives to and from the airport, my uncle Graham and my dog v Jessie for cheering me up on rainy days, and my sister Nicole for letting me appropriate many of her clothing pieces. The life of an impoverished student is not an easy one. Most of all, thank you to my parents for their love and support throughout this process. You pushed me to keep focused and continuing to make progress, even when my brain was so tired I just couldn‟t conceive of spending yet another day pounding away at that keyboard. It is over now and I can look forward to a new chapter in my life. vi Table of Contents Approval .......................................................................................................................... ii Abstract .......................................................................................................................... iii Acknowledgements ........................................................................................................ iv Table of Contents ...........................................................................................................vii List of Tables ................................................................................................................... x List of Figures................................................................................................................. xi List of Acronyms ............................................................................................................ xiii Chapter 1. Introduction.............................................................................................. 1 1.1. Research Questions ............................................................................................... 4 1.2. Data Sources and Methodology .............................................................................. 5 1.3. Thesis Outline ........................................................................................................ 7 1.4. Findings .................................................................................................................. 9 Chapter 2. Literature Review on Northern Fur Seal ............................................... 14 2.1. Introduction ........................................................................................................... 14 2.2. Taxonomic Classification ...................................................................................... 17 2.3. Distribution, Breeding, Migration, and Foraging Behaviour ................................... 18 2.4. Population Dynamics ............................................................................................ 25 2.5. Population Genetic Structure Dynamics of Northern Fur Seal ............................... 30 2.6. Summary .............................................................................................................. 37 Chapter 3. Analysis of Genetic Data: Phylogenetics and Population Genetics ................................................................................................. 39 3.1. Introduction ........................................................................................................... 39 3.2. Evolutionary Concepts .........................................................................................
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