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By Kathryn E. Mickle UNRAVELING THE SYSTEMATICS OF PALAEONISCOID FISHES—LOWER ACTINOPTERYGIANS IN NEED OF A COMPLETE PHYLOGENETIC REVISION by Kathryn E. Mickle Submitted to the Department of Ecology and Evolutionary Biology and the Faculty of the Graduate School of the University of Kansas in partial fufillment of the requirements for the degree of Doctor of Philosophy ___________________________________________ Hans-Peter Schultze, Co-Chair ___________________________________________ Edward O. Wiley, Co-Chair ___________________________________________ Linda Trueb ___________________________________________ Sharon Billings ___________________________________________ Bruce Lieberman Date Defended: April 10, 2012 The Dissertation Committee for Kathryn E. Mickle certifies that this is the approved version of the following Dissertation: UNRAVELING THE SYSTEMATICS OF PALAEONISCOID FISHES—LOWER ACTINOPTERYGIANS IN NEED OF A COMPLETE PHYLOGENETIC REVISION Committee: ___________________________________________ Hans-Peter Schultze, Co-Chair ___________________________________________ Edward O. Wiley, Co-Chair ___________________________________________ Linda Trueb ___________________________________________ Sharon Billings ___________________________________________ Bruce Lieberman Date Approved: April 10, 2012 ii ABSTRACT Actinopterygian fishes are the most diverse and speciose vertebrates on the planet. Lower actinopterygians, or fishes basal to teleosts, are critical to our understanding of the early evolution of this group, but extant lower actinopterygians are only represented by a few species. A larger diversity is preserved in the fossil record, but these fishes are poorly understood. This dissertation focuses on a subset of the extinct diversity; palaeoniscoid actinopterygians. The term “palaeoniscoid” has been used to refer to a large paraphyletic grouping of fossil fishes ranging from the Devonian to the Cretaceous. Our poor understanding of the diversity and relationships of palaeoniscoids reflects the many taxa of palaeoniscoids that remain to be described and included in phylogenetic analyses, as well as our understanding of morphological characters amongst lower actinopterygians. The main goal of this dissertation is to dismantle the paraphyletic grouping of palaeoniscoid fishes by concentrating on reassessments of morphological characters, descriptions of new taxa, and phylogenetic analyses of a vast number of taxa from the Devonian to the recent using both parsimony and Bayesian methodologies. Chapter One gives a taxonomic review of lower actinopterygians and discusses obstacles that must be overcome in order to form stronger hypotheses of relationships for palaeoniscoids. These obstacles are then addressed in the subsequent chapters. Chapters Two and Three are investigations into morphological characters. Chapter Two examines the preoperculum, a cheek bone considered important in the evolution of actinopterygians. Chapter Three presents problems with how the bones in the snout of lower actinopterygian fishes have been identified and proposes a new identification and nomenclature scheme for the bones of the snout. Chapters Four and Five are descriptions of new taxa from the Carboniferous of Utah and New Brunswick, Canada. Lastly, Chapter 6 presents results of phylogenetic analyses of lower actinopterygians. iii The data matrix analyzed incorporates the findings from the previous chapters with the addition of new characters, character states, and taxa. This matrix represents the largest analysis to date of lower actinopterygian fishes, and the first time Bayesian methodology is used to investigate the relationships of palaeoniscoid fishes. Results of both methodologies are compared to each other and previously published hypotheses. Most importantly, analysis of this matrix has resulted in the recovery of a monophyletic Paleonisciformes. The results of this chapter suggest that palaeoniscoid actinopterygians represent a natural grouping. iv ACKNOWLEDGMENTS Many people were influential in making my dissertation research possible. First, I have to thank my advisors, Hans-Peter Schultze and Ed Wiley. I was so fortunate to be looking for a graduate program the year Hans-Peter was returning to Kansas and that he and Ed were willing to take on a fossil fish student. Having co-advisors who are leaders in the fields of paleoichthyology and ichthyology was an incredible opportunity. I also have to thank my committee members Linda Trueb, Sharon Billings, and Bruce Lieberman for all of their support, encouragement, and advice. I especially have to thank Linda for all of her help with grant writing. A special thank you must be given to my advisor Ed Wiley. Not only is Ed incredibly helpful in discussing topics dealing with phylogenetics, systematics, and ichthyology, but he is one of the strongest supporters of students; he was always there for me. Ed made the ichthyology division a great place to work, learn, and in general, be a student. Ed is retiring this year and I feel lucky to have been one of his last official graduate students. I am so appreciative and thankful for the mentoring I have received from Hans-Peter Schultze. My growth as a paleoichthyologist is because of him and his advisement. I could not have asked for a more supportive advisor. He is a role model for how to be a researcher and advisor. I am going to really miss being able to pop into his office to talk about fossil fish and other things. I am so glad, honored, and excited to be working with him in the future. I have to give a special thanks to Gloria Arratia, who was, and is, incredibly helpful, influential, and supportive. I have learned much from her, and I will always consider her to be an advisor, mentor and role model. v Working in the Ichthyology division has been a wonderful experience. I was able to interact with experts like Gloria Arratia, Andy Bentley, C. Richard Robins, and Ed Wiley. The Ichthyology division also provided me with built-in colleagues and friends. I am grateful for the advice I have received from, and the friendships I have formed with, fellow Ichthyology students and post docs, Francine Abe, Pingfu Chen, Anna Clark, Matt Davis, Shannon DeVaney, Mike Doosey, Sarah Gibson, Nancy Holcroft-Benson (and Ben Benson), and Hannah Owens. I also have to thank fellow graduate students Anthony Barley, Andrea Crowther, Charles Linkem, and Jamie Oaks for research advice. Because I work on fossil fish, I was lucky enough to be part of the Vertebrate Paleontology division. I thank Larry Martin, Desui Miao, Dave Burnham, and Amanda Falk for all of their support and advice. I am very happy to be part of the strong Vertebrate Paleontology tradition at the University of Kansas. The graduate students in the museum and the department have been my Kansas family. There are too many names to mention here, but I am very lucky to have interacted with this cohort, and am grateful for the friendships formed with many of these students. Many of these friends have been so supportive to me in incredibly hard times and I know these are friendships that will outlast us moving away from graduate school. I have to thank Nate Ruhl for all of his support and advice, and listening to me, all from another time zone. Along a different line, I look at my dissertation as being a type of Phoenix. Out of the rubble of my first proposal came what is presented here in the following six chapters. Though I did not see how things would work at the time, I can look back on everything now and say I am proud of how my dissertation turned out. I must also say to Hans-Peter, Ed, and Gloria that it vi was easier for me to pick myself up by my bootstraps knowing that I had giants behind me, believing in me, and pulling me back up. Thank you. Also in terms of my research, I have to thank numerous people at many different museums for access to, and loans of, specimens. These people include David Stricklan at Brigham Young University, Steve Cumbaa and Margaret Currie at the Canadian Museum of Nature, David Berman and Amy Henrici at the Carnegie Museum of Natural History, Jessica Cundiff and Farish Jenkins at the Museum of Comparative Zoology, Harvard, Randy Miller and Michelle Hébert at the New Brunswick Museum, Spencer Lucas and Justin Spiellmann at the New Mexico Museum of Natural History and Science, Ted Cavender and Marc Kibbey at the Ohio State Museum of Biological Diversity, and Daniel Brinkman at the Yale Peabody Museum. I also have to thank Ted Cavender, Lloyd Gunther, and Dave Stricklan for donating specimens to the University of Kansas Vertebrate Paleontology collections. My research has benefitted from numerous funding sources from within the University of Kansas. I have to thank the Department of Ecology and Evolutionary Biology for travel funds to present at conferences, as well as nominating me for a Summer Research Fellowship from the Office of Research and Graduate Studies at the University of Kansas. I would like to thank the Office of Research and Graduate Studies for the Summer Research Fellowship that allowed me to make trips to museums in the summer of 2010. The University of Kansas Natural History Museum and Biodiversity Institute’s Panorama Small Grant program has funded a substantial part of my dissertation research and allowed me to participate in paleontological fieldwork, attend and present at meetings, and travel to museums to examine specimens. I was fortunate enough to receive external funding that helped make my dissertation research possible. External funding came from the Ernst Mayr Travel Grant in Animal vii Systematics from Harvard University, a travel grant from the Palaeontological Society to present at the Paleontological Congress in Beijing, and the Association of Earth Science Club of Greater Kansas City. My dissertation research was greatly improved by funding from the National Science Foundation in the form of a Dissertation Improvement Grant (DEB-1010973). I do not know how I would have been able to visit as many museums, and examine as many specimens, as I have if it were not for this grant. Last, but certainly not least, I need to thank my family—my parents, my brother, grandparents, and all my aunts, uncles, and cousins.
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