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University of California Riverside and San Diego UNIVERSITY OF CALIFORNIA RIVERSIDE AND SAN DIEGO STATE UNIVERSITY Species Delimitation and Biogeography of the Thorn Harvestmen (Acuclavella) and Their Placement Within the Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi) A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Evolutionary Biology by Casey H. Richart December 2018 Dissertation Committee: Dr. Marshal Hedin, Co-Chairperson Dr. Cheryl Y. Hayashi, Co-Chairperson Dr. Tod W. Reeder Dr. Mark S. Springer Copyright by Casey H. Richart 2018 The Dissertation of Casey H. Richart is approved: Committee Co-Chairperson Committee Co-Chairperson University of California, Riverside San Diego State University ACKNOWLEDGEMENTS We will now discuss in a little more detail the Struggle for Existence - Charles Darwin, 1859 I did not foresee how tumultuous my doctoral studies would be. This period of scientific learning was commensurately accompanied with intense personal learning. So many of you kindly broke my fall and stepped up beyond reasonable expectations. In the process you have made a life-long friend. I will be forever grateful. Thank you so much. I wish I was a poet instead of a biologist. Because of you, intense personal learning became personal growth. I love you all. Thank you to Robin Keith Hedin, Marshal Hedin, Molly Hedin, and Ole Hedin, to Kevin Burns and Kevin O'Neal, and to Shahan Derkarabetian for becoming a surrogate family when I needed it most. I don't know how to thank you; I'm crying as I reflect on your love and support. Thank you for the roof, thank you for the food, thank you for the work, thank you for your love. As my San Diego community support strengthened, so too did my family back home. To my mother and stepfather, Sheryl and Mike Fairhart I could not have finished without your support. I know I don't need to explain myself, I needed some time and you provided it. To my father and stepmother Dale Richart and Jina Bailey, thank you for providing a shelter from the storm, for making me feel comfortable and at home. To my sister and brother-in-law Poppy and Ian Louthan, thank you for flying down here just to help me move, thank you for checking in on me more iv than anyone, and for being patient and sympathetic. To Tyler, thank you for your loyal support and the Ph.inished mug! To Nick, your decisions to turn your life around helped me make positive decisions too; I'm proud of you, let's keep at it. To my brother and sister Jason and Allegra Lampley, thank you for being unwavering in your love and support. Teri and Barry Armstrong, Janice Chaufty, and Bill and Vicki Leonard - I clearly could have gone to any of you for as much support as I needed, thank you. Thanks to my nieces and nephews Hunter, Lily, Azalea, Bayani, Archer, and Vera - Sit tibi semper habetis mirantibus in cordibus vestris, et multa adventures cochlea. Thanks to B.J. Stacey for offering me a roof and for the time we spent giving thanks to the cathedral of Mother Nature's beauty. Vanesa Margarita Ramírez Bello, Cariño, gracias por tu apoyo y por la confianza que me has dado. Dr. Salu Elizabeth John, MD was integral to getting my life back on track, thank you so much. Recently, many dear friends and family reached out with personal support, and I love them for it: Courtney Achenbach, James Barklage, Elizabeth Beckett, Mike Burger, Mercedes Burns, Jay and Heidi Carlisle, Julie Charernsuk, Kimberly Cole, Caleigh Cornell, Aghop and Armine Der-Karabetian, Niccolo Eck, Jeff Fairhart, Sam Fellows, Rebecca Godwin, Marc Hayes, Steve Herman, Miguel Hernandez-Patricio, Dovi Kacev, Paul Maier, Seabird McKeon, Tyler Kai LoRusso, Tara Luckau, Makenzie Mabry, Andre Nguyen, Cassie O'Hara, Niki O'Neal, Ketan Patel, Amy Porter, Rosalyn Price-Waldman, Ty Roach, Jason Ryberg, Jordan Satler, Emily Schisler, Rachel Shoop, Lee Simpson, Eric Stiner, Alexandra Sumarli, Jill Sundlof, Nick Vinciguerra, Michael Wall, Marlene Wagner, and Yue Zhang. Thank you to All Classical Portland and its contributors for the v solace, alleviated stress, and increased productivity, and to Igor Stravinsky for making things Rite. I would like to thank Anderson.paak for reminding me to let it go and Celebrate while I still can. My advisers Marshal Hedin and Cheryl Hayashi are extraordinary persons, and I am deeply honored to be of their academic legacy. Marshal, you are better at life than anyone I know. Your research improves each year, your ability to stay current with theory and technology astounds me. All the while, you regularly get in the field and are among the best naturalists I have ever met. You perceive beauty in so many corners of life, and are incredibly adept at sharing this beauty with all around you - in the classroom, in the lab, even on the internet available to everyone. You are a caring and devoted husband and father. Because of your example I am better at life. I will always be grateful. Cheryl, thank you for showing me how it's done. Your words are powerful and they are always in my head. Your insight is sharp - always saying the right thing at the right time. I am almost always glad to hear it :- ). Also, thanks for always referring to my grammatical and spelling errors as "typos". I was fortunate to be surrounded by many excellent educators. I am particularly appreciative of my year at UC Riverside, and the academic atmosphere of evolution and systematics under the tutelage of David Reznick, Mark Springer, and John Gatesy. Many students from that time too worked hard at their academics, and I fondly recall debating Michael Forthman and John Hash on the topic of the day. A number of undergraduate students and advanced high school interns helped collect and manage data: thank you very much to Stas Vidyakin for taking images and sorting specimens, Alexa Feist for vi characterizing transcriptome alignments and field work, Lisa Kairy for curatorial duties, Rebecca Friedrich and Teta Charernsuk for help collecting morphometric data, Yixuan Xia for georeferencing and DNA extractions, and Amy Downey for morphometric data collection and data entry. Wet lab work was facilitated with the support and tutelage of Mercedes Burns, Shahan Derkarabetian, Andrew Gottscho, James Starrett, and Megan Morris. Also, thank you to the Dinsdale Lab, Rohwer Lab, and Reeder Lab for providing access to laboratory equipment. Thank you Adrienne Fusek for tuition waivers. Thank you and in solidarity with current and former lab mates Tierney Bougie, Brendan Boyer, Allan Cabrero, Dave Carlson, Erik Ciaccio, Angela DiDomenico, Kristen Emata, Erika Garcia, Jordan Satler. I am appreciative to philosophical waxing during conversations with Nate Robinett. Jordan Satler, you always helped when I needed it, thanks bud. Thank you Sean Harrington for helping to trouble-shoot phylogenetic analyses and being receptive when I needed to bounce ideas off of someone. Shahan Derkarabetian, Timothy Shaw, and Paul Maier helped troubleshoot initiating various analyses, thank you. A big thanks to Joe Warfel who helped with the beautification of multiple presentations. Discussions with William Shear improved my appreciation for the importance of a name for the retrieval of biological information, also thanks for helping identify Taracus specimens for chapter 1. I thank the blogger valen for their very useful entry (http://populationgeneticsnotes.blogspot.com/2013/07/how-to-run-structure- structure.html ) on using STRUCTURE and downstream applications. Axel Schönhofer and Jochen Martens provided Ischyropsalis genomic material. Shahan Derkarabetian, Jim Starrett, and Amy Hubert aided in RNA extractions, and S. Derkarabetian and Dave vii Carlson aided in transcriptome assembly. This research was improved via discussions with Kevin Burns, Dean Leavitt, John Gatesy, Rob Meredith, Tod Reeder, Bill Shear, Mark Springer, and J. Starrett. I thank Jean Valjean for asking tough questions. Specimens were collected with aid from D. Carlson, S. Derkarabetian, Damian Elias, Marc P. Hayes, S. Huber, Robert Keith, Paul Marek, Steve Merkley, T. Novak, Adrienne Richart, Dan Richart, Jordan Satler, A. Schönhofer, L. Slana, J. Starrett, B. Shear, and Jeff Underwood. Chapter 1 was improved through comments from Mercedes Burns, Allan Cabrero, D. Carlson, S. Derkarabetian, K. Emata, J. Starrett, and two anonymous reviewers. Chapter 1 was funded in part by the University of California Riverside Newell Travel Award, and the American Arachnological Society Vincent Roth Fund for Research in Systematics. Some data collection was supported by a California State University Program for Education and Research in Biotechnology (CSUPERB) grant to M. Hedin. viii DEDICATION I dedicate this dissertation to my teachers, for they have defined my perception of beauty, and to my students, where these definitions descend. ix ABSTRACT OF THE DISSERTATION Species Delimitation and Biogeography in the Thorn Harvestmen (Acuclavella) and Their Placement Within the Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi) by Casey H. Richart Doctor of Philosophy, Graduate Program in Evolutionary Biology University of California, Riverside, joint with San Diego State University, San Diego December 2018 Dr. Marshal Hedin, Co-chairperson Dr. Cheryl Hayashi, Co-chairperson This dissertation lays the foundation for a research program that highlights the important contribution that poorly-dispersing short-range endemic (SRE) organisms can have on advancing empirical and theoretical evolutionary biology. Here, SREs are represented by members of the harvestmen (Opiliones) superfamily Ischyropsalidoidea. In Chapter 1, phylogenetic analyses of an ancient rapid diversification at the base of Ischyropsalidoidea uncovers considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and incomplete lineage sorting is rejected as the sole contributor to gene tree conflict. In Chapter 2, an integrative taxonomy tests existing, and puts forward novel species-level taxonomic hypotheses within the Acuclavella species endemic to the inland temperate rainforest of the U.S.
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