THE EVOLUTIONARY HISTORY AND PRESERVATION OF MELANINS AND MELANOSOMES A Dissertation Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Jennifer A. Peteya August, 2018 THE EVOLUTIONARY HISTORY AND PRESERVATION OF MELANINS AND MELANOSOMES Jennifer A. Peteya Dissertation Approved: Accepted: ______________________________ ______________________________ Advisor Program Director, Integrated Bioscience Robert Joel Duff Hazel A. Barton ______________________________ ______________________________ Co-Advisor/Committee Member Interim Dean of the College Matthew D. Shawkey Linda Subich ______________________________ ______________________________ Committee Member Dean of the Graduate School Liliana D’Alba Chand Midha ______________________________ ______________________________ Committee Member Date Julia A. Clarke ______________________________ Committee Member John M. Senko ii ABSTRACT Melanins are a class of ubiquitous pigments that provide not only coloration to the organisms in which they produced, but also serve as a mechanism for thermoregulation, protection from ultraviolet radiation and cytotoxicity induced by free radicals, as well as numerous other beneficial roles. In most animals, melanins are housed in organelles called melanosomes. Melanosome morphology correlates with melanin-based coloration in birds and mammals, but melanosome diversity is limited in basal amniotes. Approximately 10 years ago, the study of melanosomes, melanin, and coloration was extended to the fossil record by the reinterpretation of microbodies preserved in fossil feathers initially interpreted as bacteria as remains of melanosomes. However, despite countless lines of evidence for this hypothesis that have been described since, some authors argue that the bacterial hypothesis is equally parsimonious. This dissertation will address some of the concerns of purveyors of the bacterial hypothesis and discuss the evolutionary history of melanosomes and melanins. We first tested the hypothesis that striped fossil feathers are the result of bacterial preservation through taphonomic experimentation. We found that modern keratinolytic bacteria preferentially colonize unpigmented stripes in modern feathers over melanized stripes, so it is unlikely that this hypothesis was supported in ancient ecosystems. We also found that bacteria and biofilms preserved in association with fossil integument are dissimilar to microbodies interpreted as fossil melanosomes. iii We began the second part of this dissertation by describing an enantiornithine bird that exhibits a mix of juvenile skeletal characteristics and sexual ornaments. Melanosomes preserved in its feathers are similar in morphology and arrangement to those in modern iridescent feathers, which are predominantly used to attract mates. We also described melanosomes associated with the fossilized skin of amphibians and lampreys, which do not exhibit diverse melanosome morphologies. Convergent shifts in melanosome diversity in mammals and pennaraptoran dinosaurs may have occurred due to changes in physiology between these two groups and their ancestors. Finally, we reviewed the functions of melanins in modern organisms and evidence for these functions in the fossil record. Based on their modern ubiquity, we hypothesized that melanin may have evolved early in the history of life. iv DEDICATION This work is dedicated to the former instructors that encouraged and inspired me to continue pursuing paleontology: my mom, who taught me how to look for fossils when I was about three years old; my dad, who decided to spend family vacations looking for fossils and going to museums in Nova Scotia; my second and third grade teachers, Judy Chester and Dorothy Ramsey, who embraced my love of paleontology and encouraged me to continue; Connie Hubbard, my high school Science Experimental Research Program (SERP) instructor, who let me do a project on dinosaurs rather than a typical experimental project; Dr. Lee Gray, my soft rock geology professor who mentored me throughout college and encouraged me to apply to do research in Mongolia; Joel Collins, my undergraduate drawing instructor who never got tired of seeing dinosaurs or trilobites in my work; my graduate paleobiology professor, Dr. Bill Ausich, who encouraged me to press on throughout my master’s studies; and finally my master’s advisor, Dr. Loren Babcock. v ACKNOWLEDGEMENTS First, I would like to thank my former advisor, Dr. Matthew Shawkey, for his patience, encouragement, help, and everything else he has given me for the past five years. I would also like to thank Dr. R. Joel Duff for taking over the role as my advisor since Dr. Shawkey moved to Belgium and my other committee members, Dr. Liliana D’Alba, Dr. Julia Clarke, and Dr. John Senko. Dr. D’Alba not only helped Nick Justyn and me with the statistical analysis in Chapter 2, but has also served as a source of encouragement and inspiration throughout my dissertation. Similarly, Dr. Clarke also served as a source of inspiration and was especially instrumental in the production of Chapter 4. Additionally, I would like to thank my current and former labmates, Nick Justyn, Dr. Brani Igic, Dr. Bill Hsiung, Dr. Ming Xiao, Asritha Nallapaneni, Dr. Chad Eliason, Dr. Rafael Maia, Weiyao Li, Xiaozhou Yang, Mario Echeverri, Dr. Daphne Fechyr- Lippens, and Jiuzhou Zhao. I served as Nick’s mentor for his undergraduate honors thesis, throughout which we co-wrote Chapter 2, and has helped with Chapter 6. He has been a great friend for the past four years and has helped me through some of the toughest times throughout the completion of this project. Chad and Rafael taught me the basics of R programming, Brani and Chad both helped me with statistical analyses, Ming helped me learn how to use Origin Pro and Igor Pro, and each one of my labmates has helped with editing my manuscripts, bouncing ideas, and moral support. vi I would also like to thank several other people instrumental in the completion of my dissertation. Dr. Quanguo Li from the China University of Geosciences and Dr. Ke- Qin Gao from Peking University provided specimens and guidance for Chapters 4 and 5. Dr. Zhorro Nikolov, Dr. Bojie Wang, Thomas Quick, and Dr. Richard Londraville provided access to and training on the Raman spectrometer, field-emission SEM, environmental SEM, and spectrophotometer, respectively. Dr. Kevin Abbasi from Case Western Reserve University provided the ToF-SIMS analysis for Chapter 3. Scott Thomas, Matt Bos, and Dr. Peter Niewiarowski provided modern amphibian and lizard samples for Chapter 5. The late Dr. Edward Burtt provided Bacillus licheniformis for the Chapter 2 experiment and for comparative Raman spectroscopy. Prasad Raut provided carbon black samples and Dean Pearson from the Pioneer Trails Regional Museum provided the Platanus specimen. Drs. Zhiheng Li, Xia Wang, Sally Thomas, and an anonymous reviewer provided criticism and feedback for Chapter 4, which is published in Palaeontology. Anonymous reviewers also improved Chapter 2, which is published in The Auk. Drs. Loren Babcock, Baoyu Jiang, and Fangchen Zhou provided helpful discussion and criticism for Chapter 3. Lastly, I would like to thank my family members for their continued support throughout my pursuit of science, including my parents, Karen and Dennis Peteya, and my husband, Dan Lopez. I would especially like to thank my sister, Dr. Stephanie Peteya, who after completing her undergraduate degree at the University of Akron suggested I contact Dr. Shawkey about working on fossil color for my Ph. D. vii TABLE OF CONTENTS Page LIST OF TABLES ............................................................................................................. xi LIST OF FIGURES .......................................................................................................... xii CHAPTER I. INTRODUCTION ............................................................................................................1 II. PREFERENTIAL ATTACHMENT AND COLONIZATION OF THE KERATINOLYTIC BACTERIUM BACILLUS LICHENIFORMIS ON BLACK AND WHITE STRIPED FEATHERS.....................................................................6 Introduction .......................................................................................................6 Material and Methods .......................................................................................8 Results .............................................................................................................14 Discussion .......................................................................................................15 III. MICROBIAL BIOFILMS PRESERVED WITH FOSSILIZED CHORDATE INTEGUMENT ARE DISTINCT FROM FOSSIL MELANOSOMES ...............20 Introduction .....................................................................................................20 Material and Methods .....................................................................................22 Results .............................................................................................................26 Discussion .......................................................................................................33 IV. THE PLUMAGE AND COLORATION OF AN ENANTIORNITHINE BIRD FROM THE EARLY CRETACEOUS OF CHINA ..............................................38 viii Introduction .....................................................................................................38