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Tyler David Nelson Temporal isolation and genetic divergence in the Choristoneura fumiferana species complex by Tyler David Nelson 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 © Tyler David Nelson, 2019 Abstract Temporal isolation contributes to ecological speciation in a diversity of insect taxa. Such prezygotic isolation can reduce or stop hybridization between closely related taxa or populations, leading to speciation. Within the spruce budworm (Choristoneura fumiferana) species complex, hybridization between species occurs freely in laboratory settings but hybrids are rarely found in the wild. Temporal isolation has been suggested as a mechanism that reduces their hybridization, but this has not been assessed for members of the complex that interact in west-central Alberta and adjacent British Columbia. I sought to determine whether temporal isolation reduces hybridization between C. fumiferana and C. occidentalis biennis, using ddRADseq to genotype 261 individual Choristoneura collected over two years. I found that C. fumiferana and C. o. biennis have significantly different flight peaks, partially due to post-diapause degree-day requirements. However, adults of these taxa contact each other with sufficient frequency to allow hybridization at an estimated rate of 2.9%. I did not find significant genetic differentiation between the even- and odd-year cohorts of C. o. biennis. Additionally, collections of C. o. biennis extended at least to Elk Island National Park in central Alberta, which is more than 100 km further east than previously recognized. In conclusion, temporal isolation likely contributes to the maintenance of genomic integrity between species of spruce budworm, but the role of other mechanisms should also be investigated. ii Acknowledgements The path taken while completing a graduate degree is not one that is travelled alone. I have many individuals to thank, but the constant overseer of this project has been my supervisor, Felix Sperling. Without your guidance, I would not have become the bug nerd that I am today, nor would I have had the opportunity to spend quite so much time discovering Alberta and its wonderful Lepidoptera (including the little brown moths!) There are numerous members of the Sperling Lab, both past and present, who deserve more than a simple thanks. Zac MacDonald, Erin Campbell, Brittany Wingert, Victor Shegelski, Rowan French, Janet Sperling, Stephen Trevoy, Bryan Brunet, Lisa Lumley, Gwylim Blackburn, Giovanny Fagua, Pasan Lebunasin Arachchige, Julian Dupuis, Heather Leibel, Kyle Snape, Marnie Wright, Christianne Nylund, and Sarah Leo have each made contributions to this project that cannot be explained in the meager space offered here. Thank you, everyone. Of course, there were many others who I met along the way who each contributed to the completion of the degree. Mike Kokich, Andrew Cook, Nick Grocock, Ronald Batallas, Caroline Whitehouse, Jonathan Backs, Kelsey Jones, Maggie MacDonald, Antonia Musso, Dylan Sjolie, Valerie Marshall, Federico Riva, Oksana Vernygora, Mónica Higuera, Ashton Sturm, Monica Kohler, and Angela Phung each had valuable input during the project. To the research scientists and professors that set me on the path to this graduate degree, notably Jon Sweeney, Jessamyn Manson, Kirk Hillier, and Deb Moreau, I thank you. To members of the Alberta Lepidopterists’ Guild, namely Charley Bird, Greg Pohl, Dave “Fizzy D” Lawrie, Gerry “Blue Wizard” Hilchie, John Acorn, Gary Anweiler, Loney Dickson, Vic Romanyshyn, Hilary Pittel, Bruce Christensen, Bob Parsons, Colleen Raymond, and Gerald Romanchuk, thank you for allowing a junior butterfly enthusiast among your ranks. iii I would also like to thank the members of my committee, Maya Evenden and Carol Frost. Your hard work is appreciated, as is your willingness to participate in a thesis defence in early August. Maya, thank you for allowing me to borrow your lab’s Unitraps, hexane, and HOBO data loggers. This project would not have happened without your generous contributions. I must also thank the 8,289 spruce budworms that dutifully gave their lives for the good of this thesis. Your SNPs will be used in future projects to help us understand you. Finally, my family deserves the utmost thanks for their love and support during the completion of this degree. Hayley, Mum, and Dad – I am grateful for each of you. And Al, thanks for being you. I can’t imagine I would have made it through this degree had we not been together in Edmonton. This project was funded by a Natural Sciences and Engineering Research Council of Canada Discovery Grant awarded to Felix Sperling. Collection permits were granted by the Alberta Provincial government (Permits 17-123, 18-598). Roger Lévesque and Michel Cusson provided access to the Choristoneura fumiferana draft reference genome to which DNA sequences were aligned. iv Table of Contents Abstract .......................................................................................................................................... ii Acknowledgements ...................................................................................................................... iii List of Tables .............................................................................................................................. viii List of Figures ................................................................................................................................ x List of Abbreviations .................................................................................................................. xii Chapter 1: Introduction and Thesis Objectives ......................................................................... 1 General Introduction ........................................................................................................ 1 The Spruce Budworm (Choristoneura fumiferana) Species Complex .......................... 2 Temporal Isolating Mechanisms Among Choristoneura spp. ....................................... 5 Pheromone Isolating Mechanisms Among Choristoneura spp. .................................... 8 Mechanical Isolating Mechanisms Among Choristoneura spp. .................................. 10 Larval Host-Associated Isolating Mechanisms Among Choristoneura spp. .............. 11 Thesis Objectives ............................................................................................................. 12 References ........................................................................................................................ 14 Chapter 2: Temporal isolation and genetic divergence between spruce budworm moths (Choristoneura fumiferana and C. occidentalis) in west-central Alberta and British Columbia ...................................................................................................................................... 29 Introduction ..................................................................................................................... 29 Methods ............................................................................................................................ 32 Sampling ............................................................................................................... 32 DNA Extraction and ddRADseq............................................................................ 34 v DNA Data Processing ........................................................................................... 35 Taxonomic Identifications ..................................................................................... 36 Evaluation of Temporal Isolation ......................................................................... 38 Genomic Location of SNPs ................................................................................... 39 Results .............................................................................................................................. 40 Collections ............................................................................................................ 40 ddRAD SNPs ......................................................................................................... 41 Identity of Taxa and Hybrids ................................................................................ 41 Temporal Isolation Within and Between Species.................................................. 43 Range Extension of C. occidentalis biennis .......................................................... 44 Identity and Location of High-loading SNPs ........................................................ 44 Discussion......................................................................................................................... 45 Confirmation of Hybridization Between fum and C. occidentalis ........................ 45 Temporal Isolation Within and Between Species.................................................. 45 Association of Temporal Isolation and Accumulated Degree-days ...................... 48 Isolation Between and Within Subspecies of C. occidentalis ................................ 49 Adaptive SNPs and Preliminary Genomic Architecture ....................................... 50 Evolution of C. o. biennis ...................................................................................... 51 Conclusion ......................................................................................................................
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