Systematics of lower Cyclorrhaphan Diptera, with an emphasis on Syrphidae by Andrew Young A thesis submitted to the Faculty of Graduate and Postdoctoral Affairs in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Carleton University Ottawa, Ontario © 2018 Andrew Young Abstract This doctoral thesis is presented in three chapters. The first chapter is a phylogenetic analysis of the lower Cyclorrhaphan (Insecta: Diptera) families of Diptera. These families form a paraphyletic grade, and have been a long-standing problematic assemblage of the Dipteran tree of life. We attempted to bring resolution to this assemblage of families using a combination of transcriptomic and anchored hybrid enrichment data from 43 ingroup taxa. Results were largely concordant with existing molecular phylogenetic efforts, but Lonchopteridae remains problematic to place. The second chapter of the thesis is a more detailed phylogenetic analysis of a single lower Cyclorrhaphan family, the Syrphidae. This chapter has also been published as an open-access paper in BMC Evolutionary Biology. Subfamilial boundaries within Syrphidae are a known problem, and there has been little consensus on how to treat the paraphyletic subfamily Eristalinae. We used a novel anchored hybrid enrichment probe kit to produce a 30 species phylogeny of Syrphidae with strong support values across the entire tree. As expected, a paraphyletic Eristalinae was recovered. Our sampling was not rigorous enough to produce a stable revised classification, but we hope this chapter will act as a starting point for a future reclassification of the subfamily. This chapter has been published as an open-access paper in BMC Evolutionary Biology. The final chapter of the thesis was also Syrphidae-focused, with a taxonomic revision of the Australian Psilota. The revision is based on a combination of Cytochrome c Oxidase I DNA barcodes and morphological analysis. The number of known Australian Psilota species was increased from 14 to 30, with two acknowledged species complexes ii that should be revisited in the future. All species are fully described and illustrated, with external habitus and male genitalia photographs. iii Preface: The first and third chapters of this thesis are unpublished manuscripts. The second chapter, “Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)” is published in BMC Evolutionary Biology. This publication is here reproduced in full (with the exception of supplementary tables, where a link to the freely-available publication is instead provided due to their length), and was published as an open-access paper with the authors retaining full copyright of the article. This was a co-authored publication, and full contributions of all authors are listed at the beginning of the chapter. The full bibliographic information for this chapter is as follows: “Young, A. D., A. R. Lemmon, J. H. Skevington, X. Mengual, G. Ståhls, M. Reemer, K. Jordaens, S. Kelso, E. M. Lemmon, M. Hauser, M. De Meyer, B. Misof and B. Wiegmann (2016). "Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)." BMC Evolutionary Biology 16(1): 143.” As one of the lead authors on this paper, I was fully involved in setting up and conducting the research, obtaining data, and analyzing results, a well as preparing and writing the material presented in the thesis. Specifically, I have expressed an interested in Syrphidae phylogeny to Dr. Jeff Skevington since at least 2012, and have been interested in approaching it using molecular methods. I was responsible for identifying all Syrphidae voucher specimens used in the analysis, and I analyzed and compared the phylogenetic tree generated from our dataset to all published syrphid phylogenies. All parts of the second chapter were written by me except for iv the original methods section, which was written by Alan and Emily Lemmon (who pioneered this specific target enrichment technique). Full details of all author contributions are noted at the beginning of chapter 2. Supervisor’s statement: All of the above information is correct. Andrew has been involved in discussions of Syrphidae phylogenetics with my lab since completing his M.Sc. in 2012, and was fully involved in conducting the research, obtaining data, and analyzing the results of the phylogenetic analysis, as well as preparing and writing the material provided in the thesis (except where noted above). v Acknowledgements Friends, family, and colleagues too numerous to mention were instrumental in the successful completion of this thesis, many of whom were invaluable to me as both emotional and academic support. On an academic front, I would like to thank the 1KITE and North Carolina State University labs for providing sequences used in the first chapter of the thesis, and Oliver Niehuis and Berhard Misof for teaching the bioinformatics course that was invaluable to me during data analysis. Wouter van Steenis and Chris Thompson’s insights into Australian Psilota taxonomy were also invaluable, especially when I was first starting out with the group. Keith Bayless, Chris Thompson, Trevor Burt, Ximo Mengual, and the entire Australian Museum, Queensland Museum, and Australian National Insect Collection Diptera units all kindly hosted me during lab visits at various points in my thesis, some of them in their own homes. Jim O’Hara, Jeff Cumming, Brad Sinclair, Michelle Locke, Owen Lonsdale, Scott Kelso, Scott Brooks, Shannon Henderson, A.J. Fleming, and everyone else who shows up in the CNC Diptera Unit: our conversations were always enlightening, about Diptera and many other things. Joel Kits helped me run Trinity on the CNC supercomputer cluster for Chapter 1 and provided me with excellent thesis-related advice. In Taiwan, Wouter van Steenis, Jeroen van Steenis, Menno van Zuijen, Chris Palmer, and Axel Ssymank taught me more about collecting Syrphidae in three weeks than I could have learned in an entire degree on my own, while 吳宗 學 (“Bill”) was an invaluable local guide and keen collector. Morgan Jackson, Miles vi Zhang, and Adam Jewiss-Gaines are all close friends who have been working towards their doctorates simultaneously to me, and all of them have been invaluable sounding boards and sources of motivation during this entire degree. Victoria Nowell, Sebastian Namek, and Nadia Boukina were all summer students when I worked with them, and all of them saved me from mountains of databasing and other invaluable, but time consuming tasks. My external advisory committee, Julian Starr and Andrew Simons, as well as my external defence committee members, Vazrick Nazari and Nicolas Rodrigue were invaluable and provided much useful critique during and after the defence process. Finally, I’d like to thank my supervisors: Jeff Skevington for teaching me much of what I know about Syrphidae and for always providing me the opportunities I needed to succeed, and Jeff Dawson, for always being understanding of entomological complications and helping me navigate Carleton University. On a personal note, I’d like to thank all the friends who have supported me along the way, whether or not they understood or cared about whatever academic mishaps I ranted about to them. Thanks to Steve Marshall, for going out on a limb and hiring me as a M.Sc. student with no funding. An extra special thanks to my parents and brother for always being supportive of me, even when they’d rather I didn’t bring so many live animals into the house. I’d particularly like to thank my maternal grandfather, Peter McQueen, who passed away while I was collecting data in Australia. Most of all, I’d like to thank Aislinn Wyatt, my partner and better half, for always supporting me, believing in me, and generally being awesome. Hail Satan. vii Table of Contents Abstract ................................................................................................................................ ii Preface: ................................................................................................................................ iv Acknowledgements .............................................................................................................. vi List of Tables .........................................................................................................................xi List of Illustrations ................................................................................................................ xii General Introduction ............................................................................................................. 1 References .........................................................................................................................5 Chapter 1: Phylogenetics of lower Cyclorrhapha using transcriptome and hybrid enrichment data .................................................................................................................... 8 Author Contributions .........................................................................................................8 Abstract .............................................................................................................................9 Introduction ......................................................................................................................9 Materials and Methods ...................................................................................................