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Genomics of Dendroctonus Ponderosae (Coleoptera: Curculionidae) in Alberta

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Genomics of Dendroctonus Ponderosae (Coleoptera: Curculionidae) in Alberta Genomics of Dendroctonus ponderosae (Coleoptera: Curculionidae) in Alberta By Stephen Andrew Lane Trevoy A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science In Systematics and Evolution Department of Biological Sciences University of Alberta © Stephen Andrew Lane Trevoy, 2018 Abstract Rapid advances in sequencing technologies and analysis methods have greatly increased our understanding of genomic architecture in non-model organisms. The mountain pine beetle (MPB; Dendroctonus ponderosae) is a non-model organism that has received intensive genomic study and is of great economic interest in western Canada. I apply next-generation sequencing (NGS) technologies to create a library of single nucleotide polymorphism (SNP) markers, and use the markers to address basic questions concerning population structure in MPB. Then, using the same dataset, I amend standard filtering and analysis techniques for population genomics data to ask questions about genomic architecture and functional genetics. By combined use of linkage network and principal components analysis (PCA), I find new SNP markers for determining sex, and describe a novel method for finding putative islands of genomic divergence that I apply to the major Canadian populations of MPB. Finally, I validate the chromosomal contiguity of these islands of genomic divergence by generating two linkage maps for male- and female-associate sets of MPB SNPs, which I developed using a colony of lab-bred F2 sibling crosses. Both linkage analysis and the viability of experimental crosses suggest the existence of incipient speciation between populations of MPB within their Canadian range. The results described here also contribute to a reassessment of the value of cohorts of loci in tight linkage disequilibrium that have previously been viewed as unusable for population genomics studies. ii Preface The research conducted for this thesis was part of a collaborative effort led by Dr. Felix Sperling at the University of Alberta. The majority of the sampling and laboratory work was performed by me, with some samples in Chapters 2 and 3 being supplied by Dr. J.K. Janes. Chapter 2 was co-written by Janes and me, under the supervision of Sperling. Chapter 2 was published as: S.A.L. Trevoy, J.K. Janes, & F.A.H. Sperling (2018). “Where did mountain pine beetle populations in Jasper Park come from? Tracking beetles with genetics,” The Forestry Chronicle, vol. 94, issue 1, 20-24. DOI: 10.5558/tfc2018-004 I was responsible for the laboratory work, data analysis and interpretation, and for co- writing the manuscript. Janes contributed some samples, data interpretation and writing. Sperling was involved in concept formation, data interpretation and manuscript edits. Chapter 3 has been accepted for publication at Ecology and Evolution as: S.A.L. Trevoy, Janes J.K., Muirhead K., and Sperling F.A.H. “Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)”. DOI: 10.1002/ece3.4803 I was responsible for concept formation, laboratory work, data analysis, data interpretation, and writing the manuscript. Janes contributed some samples, concept formation, data interpretation and manuscript edits. Data analysis used analytical tools developed by K. Muirhead. Sperling was involved in concept formation, data interpretation and manuscript edits. iii Acknowledgements I could not have completed this project without the support of many family, friends and colleagues. First, to Dr. Felix Sperling, an able mentor and guide through this entire process. You helped me immensely in securing funding, designing the parameters of the experiments, and continued to offer guidance and support through many years of difficult analysis and writing. Thank you so much for your patience and help. Second, to Dr. Jasmine Janes, who managed to be a consistent source of encouragement and guidance throughout my masters, even after many moves and difficult time changes. Thank you to Dr. David Coltman, who was my regular thesis committee member and took time from his sabbatical to serve on my examining committee. Likewise, thank you to Dr. Changxi Li for being the arm’s length examiner. Thank you to the entire Sperling Lab, past and present: Erin Campbell, Christianne McDonald, Philip Batista, Gwylim Blackburn, Victor Shegelski, Brittany Wingert, Megan Funke, Kyle Snape, Rowan French, Tyler Nelson, Nils Koch, and honorary member, Kevin Muirhead. I would particularly like to thank Julian Dupuis for support in bioinformatics and data analysis, Giovanny Fagua for training in sample preparation, and Taylor Becker, who was invaluable for managing and maintaining the beetle colonies used to create the results for chapter 4, a monumental effort on her part. I would also like to thank Bryan Brunet, my former office mate, for his patience with me as I adjusted to graduate student life, and his tutelage while I took my first steps into command line, linkage mapping, and STRUCTURE analysis. To my family support, especially my parents, Anna and Andrew Trevoy, and my wife, Bhuvaneswary Trevoy. You three have given me the stability and support I needed to push through to the end of this project. Thank you from the bottom of my heart. To my sisters, Victoria Biel, Julia Dawe, Michelle Wiederkehr, and Jayasree Narayanan, thank you for being a family to me, and a constant source of support. And lastly, a thank you to my friends, most notably Grace Carscallen, Gabriel Boucher and Joseph Kent, who had a truck and a helping hand to offer when I needed pine logs moved. A warm thank you to Laval University’s IBIS (Brian Boyle) and University of Alberta’s MBSU (Sophie Dang) services for genotyping. We are grateful for beetle samples provided by Katherine Bleiker, Celia Boone, Jordan Burke, Barry Cooke, Mike Cunningham, Tom Hutchison, Devin Letourneau, Gillian MacDonald, Clint McCrea, Fraser McKee, Rory iv McIntosh, Brent Murray, Amanda Roe, Erica Samis, Greg Smith, Brogan Waldner, Jeff Weber, Caroline Whitehouse, and Kristen Zentner. And finally, to the Evenden Lab, past and present, but especially Maya Evenden, Caroline Whitehouse, Asha Wijerathna, Ronald Batallas, and Chetna Saran. Maya, Caroline and Asha were invaluable for showing me how to establish breeding crosses and emergence boxes. A special thank you to Jeff Johnston at the UofA Science Faculty Fabrication Lab, who helped in the construction of over seventy new emergence boxes. Field and lab work for this thesis was funded by a grant from the Natural Science and Engineering Research Council of Canada (grant no. NET GP 434810-12) to the TRIA Network, with contributions from Alberta Agriculture and Forestry, fRI Research, Manitoba Conservation and Water Stewardship, Natural Resources Canada - Canadian Forest Service, Northwest Territories Environment and Natural Resources, Ontario Ministry of Natural Resources and Forestry, Saskatchewan Ministry of Environment, West Fraser Timber Co. Ltd. and Weyerhaeuser Canada Ltd. v Table of Contents Abstract .......................................................................................................................................... ii Preface ........................................................................................................................................... iii Acknowledgements ...................................................................................................................... iv List of Tables ................................................................................................................................ ix List of Figures ............................................................................................................................... xi List of Abbreviations ................................................................................................................. xiv 1. General Introduction .................................................................................................................1 1.1 Overview of population genomics .........................................................................................1 1.1.1 Genomics and genetics .....................................................................................................1 1.1.2 Linkage disequilibrium .....................................................................................................3 1.1.3 Next generation sequencing techniques ............................................................................4 1.2 Mountain pine beetle biology .................................................................................................6 1.2.1 Ecology and life history ...................................................................................................6 1.2.2 Population genetics ..........................................................................................................8 1.3 Thesis overview ......................................................................................................................9 1.4 Literature cited .....................................................................................................................11 2. Where did mountain pine beetle populations in Jasper Park come from? Tracking beetles with genetics ....................................................................................................................19 2.1 Summary ..............................................................................................................................19
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