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Assessing the quality of the fossil record using a phylogenetic approach
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Assessing the quality of the fossil record using a phylogenetic approach
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Assessing the quality of the fossil record using a phylogenetic approach
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ASSESSING THE QUALITY OF THE FOSSIL RECORD USING A PHYLOGENETIC APPROACH by C. Henrik Woolley A Dissertation Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (GEOLOGICAL SCIENCES) May 2023 ii ACKNOWLEDGEMENTS This project would not be possible without the unwavering support of faculty, staff, and fellow students past and present in the Department of Earth Sciences at the University of Southern California (USC), nor without the generous support and encouragement from curators, collections staff, students, and volunteers in the Dinosaur Institute, Vertebrate Paleontology, Herpetology, and Entomology departments at the Natural History Museum of Los Angeles County (NHMLAC). Moreover, this project was made possible through support of numerous colleagues from museums and universities around the world. First and foremost, I would like to thank the person who has been the most singularly instrumental in advancing my career: my research advisor, Nate Smith. I do not have enough space here to highlight the entirety of the ways Nate has enhanced my life as a scientist and as a person throughout our six years working together. From helping me through a challenging transition from Boulder, Colorado to Downtown Los Angeles, to advocating for me in the middle of Antarctica during my first year of graduate school, to navigating academic progress during a global pandemic, to alerting me to myriads of outreach opportunities, to dropping everything to help me on millions of drafts of abstracts, manuscripts, grant applications, and postdoc applications, I would not be where I am today without the positivity, encouragement, and relentless support and advocacy from Nate. From the bottom of my heart and soul, thank you, Nate, for taking a chance on me back in 2016. I would also not be where I am today without the steadiness and unrelenting support of my academic advisor, Dave Bottjer. Like Nate, Dave has been fundamentally instrumental in advancing my career and helping me navigate the ups, downs, ins and outs of graduate school at USC. Dave’s consistent support, centered on his availability to meet and workshop scientific iii ideas pretty much every week for six years, and give me feedback on the myriad of class projects, presentations, talks, conference abstracts, manuscript drafts, grant proposals and postdoc applications, was crucial in my development as an academic. Whether it was snags in a research project, or excitement about the latest USC Football news and game highlights, Dave was a constant force of enthusiasm and encouragement throughout my academic career at USC. Thank you, Dave. I would also like to thank my dissertation committee members, Luis Chiappe, Frank Corsetti, and Adam Huttenlocker, for their staunch support the various projects associated with this dissertation and enlightening conversations – academic and otherwise – over the years. A special, enormous thank-you to my USC graduate student officemates past and present for including me in such a supportive, hilarious, fun, and deeply rewarding community that thinks about fossils for a living: James Beech, Shannon Brophy, Paul Byrne, Nate Carroll, Tori Cassady, Ali Cribb, Kiersten Formoso, Adit Ghosh, Amanda Godbold, Claire Johnson, Reena Joubert, Katya Larina, Emily Patellos, Priyanka Soni, Jeff Thompson, Dylan Wilmeth, and Becky Wu. I would like to thank Brian Brown and the Entomology Department at NHMLAC for access to the Keyence Microscope used for looking at tiny lizard fossil described in this study. I also thank Neftali Comacho and the Herpetology Department at NHMLAC for access to modern osteological specimens used for comparisons to fossils. Special thanks to Giar-Ann Kung (NHMLA) for assistance and feedback with generating the scanning electron micrographs from the museums scanning electron microscope. Special thanks to Alan Zdinak, Erika Durazo and Beau Campbell for invaluable help preparing fossils related to my dissertation research. Thank you to Maureen Walsh for access to specimens in the NHMLAC Dinosaur Institute Collections. iv I would also like to acknowledge that I would not be where I am today without the persistent support and enthusiasm from my supervisors, mentors, and friends I made during my time at the Denver Museum of Nature & Science prior to arriving at USC: Colleen Carter & Evelyn Busch, Joe Sertich, Carol Lucking, Dave Lawrence, Eric Lund, Mike Getty, Ian Miller, Logan Ivy, Tyler Lyson, Dave Krause, Gussie Maccracken, Kristen MacKenzie, Nicole Neu- Yagle, Natalie Toth, Salvador Bastien. Thank you all for believing in me and providing me with an unbelievable community as I navigated a new career. I would like to thank Jaelyn Eberle and Jacob Van Veldhuisen at the University of Colorado Museum of Natural History for logistical and institutional support with fieldwork related to my dissertation research. Many thanks to Randy Irmis, Carrie Levitt-Bussian, and Tylor Birthisel at the Natural History Museum of Utah for persistent support and access to specimens related to this dissertation research. Thank you to Carl Mehling at the American Museum of Natural History and Daniel Brinkmann at the Yale Peabody Museum for access to specimens related to this research. I owe so much of the success I have had at USC and NHMLAC to my friends, near and far, who have supported this dream of mine in various ways over the past ten years. A special shoutout to Will Strathmann, Jeremy Cronon, and Anna McCabe for joining me on paleontological fieldwork related to this dissertation, and finding the best fossils of the whole trip. Huge thanks to Kenny Bolster, Elaina Graham, Josh Kling, and Rin Moriyasu for allowing me to escape reality nearly weekly on our epically long Dungeons & Dragons Campaigns over the past three years. Huge thanks to Gabe Santos for fostering all of the best of my nerdy tendencies, and for opening up cool new ways to connect with people over science and stories. And thank you to Connor Abernathy, Max Arnell, Nick Lafarge, Conor Maginn, Fergus v Moynihan, James Reddicliffe, and Mia Bandoni for keeping me grounded and making me laugh so hard over these years together and apart. Thank you to my partner, Lauren, for being unimaginably supportive of this work over the years, and for providing unique opportunities to carry out my research in Flagstaff, Clarkston, Kona, Seattle, and LA as I worked from our apartment during your travel nurse contracts. You have enriched my life in so many ways, and the completion of this work is a direct result of the effort each of us has made to build each other up every day. Thank you for being curious about the world with me, from travel to wildlife spotting to camping to backpacking to just looking up at the stars. It’s all better when I’m exploring with you. I want to thank my sister, Elsa Harberg, for putting up with me over the past 30 years, and for being an incredibly supportive sibling through all of life’s challenges. Special thanks to my brother-in-law, Joey Harberg, for his enthusiastic support of my career, USC Football, and for providing critical dental tools I’ve used in uncovering fossils in the soft sediments of the Chinle Formation. This dissertation is dedicated to my parents, Karin and Charlie Woolley, for instilling in me the enthusiasm to pursue what I’m passionate about, and for fostering a love for nature and the outdoors. I’m so proud and lucky to be your son. vi TABLE OF CONTENTS Acknowledgements………………………………………………………………………………. ii List of Tables ................................................................................................................................ xi List of Figures…………………………………………………………………………............... xii Abstract………………………………………………………………………………………... xvii Chapter 1: Introduction…………………………………………………......…………................. 1 References ...................................................................................................................................... 4 Chapter 2: The preservation of phylogenetic information in the global squamate fossil record ... 7 Abstract ………………………………………………………………………………………….. 7 2.1. Introduction ....................................................................................................................... 8 2.2. Materials & Methods ...................................................................................................... 9 2.2.1. Sampling the published squamate fossil record ..................................................... 9 2.2.2. Fossil completeness metric and phylogenetic datasets .......................................... 10 2.2.3. Data visualization and statistical tests .................................................................. 11 2.3. Results ............................................................................................................................. 12 2.3.1. The completeness of the squamate fossil record through geologic time ............... 12 2.3.2. Taxonomic comparisons ........................................................................................ 15 2.3.3. Regional sampling comparisons ............................................................................ 15 2.3.4. Depositional setting and completeness .................................................................. 16 2.4. Discussion ....................................................................................................................... 18 2.4.1. Phylogenetic completeness patterns through geologic time .................................. 18 2.4.2. Effects of taxonomy/body plan on phylogenetic completeness .............................. 18 2.4.3. Effects of regional sampling biases on phylogenetic completeness ....................... 20 2.4.4. Effects of depositional environment on phylogenetic completeness ...................... 21 2.5. Conclusion ...................................................................................................................... 22 References .................................................................................................................................... 23 Figures .......................................................................................................................................... 27 Chapter 3: New fossil lizard specimens from a poorly-known squamate assemblage in the Late Cretaceous (Campanian) San Juan Basin, New Mexico, USA .................................................... 32 vii Abstract ………………………………………………………………………………................ 32 3.1. Introduction ..................................................................................................................... 33 3.2. Geologic Setting .............................................................................................................. 36 3.3. Materials & Methods ...................................................................................................... 37 3.3.1. Anatomical Terminology ........................................................................................ 38 3.3.2. Institutional Abbreviations ..................................................................................... 38 3.4. Results ............................................................................................................................. 38 3.4.1. Systematic Paleontology: Chamopsiidae indet. ..................................................... 38 3.4.1.a. Referred Specimen ........................................................................................ 39 3.4.1.b. Locality and Horizon .................................................................................... 39 3.4.1.c. Description .................................................................................................... 39 3.4.1.d. Discussion ..................................................................................................... 39 3.4.2. Systematic Paleontology: Scincomorpha indet. ......................................................40 3.4.2.a. Referred Specimen ........................................................................................ 41 3.4.2.b. Locality and Horizon .................................................................................... 41 3.4.2.c. Description .................................................................................................... 41 3.4.2.d. Discussion ..................................................................................................... 42 3.4.3. Systematic Paleontology: Scincomorpha family indet. .......................................... 43 3.4.3.a. Referred Specimen ........................................................................................ 43 3.4.3.b. Locality and Horizon .................................................................................... 43 3.4.3.c. Description .................................................................................................... 43 3.4.3.d. Discussion ..................................................................................................... 43 3.4.4. Systematic Paleontology: Odaxosaurus indet. ...................................................... 44 3.4.4.a. Referred Specimen ........................................................................................ 44 3.4.4.b. Locality and Horizon .................................................................................... 44 3.4.4.c. Description .................................................................................................... 44 3.4.4.d. Discussion ..................................................................................................... 45 3.4.5. Systematic Paleontology: “Hunter Wash” Anguidae Osteoderm Morphotype A . 46 3.4.5.a. Referred Specimen ........................................................................................ 47 3.4.5.b. Locality and Horizon .................................................................................... 47 3.4.5.c. Description .................................................................................................... 47 3.4.5.d. Discussion ..................................................................................................... 47 3.4.6. Systematic Paleontology: “Hunter Wash” Anguidae Osteoderm Morphotype B . 47 3.4.6.a. Referred Specimen ........................................................................................ 47 3.4.6.b. Locality and Horizon .................................................................................... 48 3.4.6.c. Description .................................................................................................... 48 3.4.6.d. Discussion ..................................................................................................... 48 3.4.7. Systematic Paleontology: Platynota indet. ............................................................ 49 3.4.7.a. Referred Specimen ........................................................................................ 49 3.4.7.b. Locality and Horizon .................................................................................... 49 3.4.7.c. Description .................................................................................................... 49 3.4.7.d. Discussion ..................................................................................................... 50 3.5. Discussion ..................................................................................................................... 52 viii 3.5.1. Squamate diversity and biogeography on Laramidia ............................................ 52 3.6. Conclusions ................................................................................................................... 55 References .................................................................................................................................... 55 Tables .......................................................................................................................................... 62 Figures .......................................................................................................................................... 64 Chapter 4: A biased fossil record can preserve reliable phylogenetic signal .............................. 73 Abstract ……………………………………………………………………………………........ 73 4.1. Introduction ………………………………………………………………………......... 74 4.2. Materials & Methods ...................................................................................................... 76 4.2.1. Sampling the Fossil Squamate Skeleton in Natural History Collections ............... 76 4.2.2. Measurement of Phylogenetic Signal ..................................................................... 79 4.2.2.a. Parsimony-based Phylogenetic Signal ......................................................... 81 4.2.2.b. Model-based Phylogenetic Signal ................................................................ 82 4.3. Results ............................................................................................................................. 84 4.3.1. Characterizing Bias in the Squamate Fossil Record ............................................. 84 4.3.2. Analyses of Phylogenetic Signal ............................................................................ 85 4.2.2.a. Parsimony-based Assessements of Phylogenetic Signal .............................. 85 4.2.2.b. Model-based Assessements of Phylogenetic Signal ..................................... 86 4.4. Discussion ....................................................................................................................... 87 4.4.1. Biases in the Squamate Fossil Record ................................................................... 87 4.4.2. Homoplasy and Retained Synapomorphy in the Fossil Record ............................. 89 4.4.3. Model-based Analyses of Phylogenetic Signal ...................................................... 90 4.5 A Biased Fossil Record Contains Reliable Phylogenetic Data ........................................ 94 References .................................................................................................................................. 95 Figures ........................................................................................................................................ 100 4S Supplementary Information for Chapter 4 ............................................................................ 106 Chapter 5: Unique coupling of fossil lizard diversity and skeletal completeness in the Late Cretaceous Gobi Desert offers a phylogenetic lens on lagerstätten ………………………...… 155 Abstract ……………………………………………………………………………………...... 155 5.1. Introduction ………………………………………………………………………....... 156 5.2. Results ……………………………………………………………………………....... 159 ix 5.2.1. General phylogenetic completeness of non-avian theropods, birds, and squamates ......................................................................................................................................... 159 5.2.2. Preservation of phylogenetic information in the Early Cretaceous Jehol Biota . 160 5.2.3. Preservation of phylogenetic information in the Late Cretaceous (Campanian) Gobi Desert .................................................................................................................... 161 5.2.4. Continental-scale influence of exceptional preservation on phylogenetic character data ................................................................................................................................ 162 5.2.5. Incorporation of lagerstätten taxa into phylogenetic analyses ............................ 163 5.2.6. The phylogenetic “lagerstätten effect” in a global sampling context ................. 163 5.2.7. Depositional setting and fossil squamate completeness .......................................165 5.2.8. Gobi Desert squamates compared to lagerstätten deposits ................................. 166 5.3. Discussion ................................................................................................................... 167 5.3.1. The desert dunes of the Campanian Gobi Desert: a different kind of taphonomic anomaly? ........................................................................................................................ 167 5.3.2. The “lagerstätten effect” on taxon selection in phylogenetic analyses: supply vs. demand ............................................................................................................................168 5.3.3. Quantifying the “lagerstätten effect” via a phylogenetic lens ............................. 170 5.4. Materials & Methods ................................................................................................... 171 References .................................................................................................................................. 173 Figures ........................................................................................................................................ 178 5S. Supplementary Information for Chapter 5 ........................................................................... 185 Chapter 6: Conclusions …………………………………………………………………......… 240 6.1. Chapter 2 Review ........................................................................................................ 240 6.1.1. Summary ............................................................................................................. 240 6.1.2. Future Directions ................................................................................................ 241 6.2. Chapter 3 Review ........................................................................................................ 242 6.2.1. Summary ............................................................................................................. 242 6.2.2. Future Directions ................................................................................................ 242 6.3. Chapter 4 Review ........................................................................................................ 243 6.3.1. Summary ............................................................................................................. 243 6.3.2. Future Directions ................................................................................................ 244 x 6.4. Chapter 5 Review ........................................................................................................ 244 6.4.1. Summary ............................................................................................................. 244 6.4.2. Future Directions ................................................................................................ 245 6.5. Final Thoughts ............................................................................................................ 245 References .................................................................................................................................. 246 Figures ........................................................................................................................................ 249 xi LIST OF TABLES Chapter 3 Tables Table 1. Summary of previously described squamate material from the Fruitland and Kirtland formations, including suggested changes in taxonomic referral................................................... 62 Table 2. Lizard faunas of select Late Campanian geologic units in the Western Interior of North America. Geologic units arranged in descending order of geographic location, from North to South............................................................................................................................... 63 xii LIST OF FIGURES Chapter 2 Figures Figure 1. Summary of morphology-based hypotheses of squamate evolutionary relationships, whose character datasets were used for the Character Completeness Metric 2 (CCM2) in this study.............................................................................................................................................. 27 Figure 2. Time series plots of fossil squamate data used in this study......................................... 28 Figure 3. Summary of Character Completeness Metric 2 (CCM2) distributions among squamate taxonomic groups and line drawings of representative examples of various completeness percentages............................................................................................................. 29 Figure 4. Violin plots of the distribution of squamate Character Completeness Metric 2 (CCM2) percentages per landmass and per depositional setting.................................................. 30 Figure 5. Summary of affinities between fossil lizard, snake, and amphisbaenian Character Completeness Metric 2 (CCM2) distributions and depositional environment........................................... 31 Chapter 3 Figures Figure 1. Surface exposures of the Fruitland and Kirtland formations in the San Juan Basin of northwestern New Mexico............................................................................................................ 64 Figure 2. DMNH EPV.119583, Chamopsiidae indet. jaw fragment from the “Hunter Wash Local Fauna”, Fruitland Formation............................................................................................... 65 Figure 3. DMNH EPV.119554, Scincomorpha, partial left dentary, from the “Hunter Wash Local Fauna”, Fruitland Formation............................................................................................... 66 Figure 4. DMNH EPV.119567, Scincomorpha indet. osteoderm from the “Hunter Wash Local Fauna”, Kirtland Formation................................................................................................ 67 Figure 5. DMNH EPV.119555, Anguidae posterior left dentary from the “Hunter Wash Local Fauna”, Kirtland Formation................................................................................................ 68 Figure 6. Anguidae indet. osteoderms from the “Hunter Wash Local Fauna”, Fruitland/Kirtland formations....................................................................................................... 69 Figure 7. DMNH EPV.119569, Platynota indet., jaw fragment from the “Hunter Wash Local Fauna”, Kirtland Formation.......................................................................................................... 70 Figure 8. Late Campanian latitudinal distribution of lizard groups described in this study......... 71 xiii Chapter 4 Figures Figure 1. Schematic diagram of an example squamate skeleton (modeled after Uta stansburiana), with colorized anatomical regions used in this study for sampling of fossil squamate collections, and example fossil squamate elements.................................................... 100 Figure 2. Summary of sampled squamate collections (combined in-person and electronic databases), divided by schematic diagrams of predominant fossil squamate body plans.......... 101 Figure 3. Summary of parsimony-based measurements of phylogenetic signal in the squamate fossil record used in this study.................................................................................... 102 Figure 4. Distributions of d-Statistic for the pruned GEA and SEA legged squamate character dataset.......................................................................................................................... 103 Figure 5. Distributions of d-Statistic among anatomical bins for the pruned GEA and SEA legged squamate character dataset.............................................................................................. 104 Figure 6. Distributions of d-Statistic for the pruned GEA legless squamate character dataset.. 105 Supplementary Figures Figure S1. Schematic diagram of an example squamate skeleton (modeled after Uta stansburiana, lower image), with colorized anatomical regions used in this study for sampling of fossil squamate collections, and example fossil squamate elements...................... 114 Figure S2. Workflow for keyword search-sampling Yale Peabody Museum’s electronic collections database.................................................................................................................... 115 Figure S3. Distribution skeletal elements sampled and sourced phylogenetic characters.......... 116 Figure S4. Distributions of CI and RI values per anatomical bin for the GEA dataset.............. 117 Figure S5. Distributions of CI and RI values per anatomical bin for the SEA dataset............... 118 Figure S6. Summary of parsimony-based measurements of phylogenetic signal, with character matrices and topologies swapped................................................................................ 119 Figure S7. Distributions of CI and RI values per anatomical bin for the GEA matrix vs. SEA topology dataset.......................................................................................................................... 120 Figure S8. Distributions of CI and RI values per anatomical bin for the SEA matrix vs. GEA topology dataset.......................................................................................................................... 121 Figure S9. Sample visual representations of the calculations of node probabilities................... 122 xiv Figure S10. Summary of distributions of d-Statistic values for the GEA dataset using time- calibrated fossil tips and 1 million-year uniform branch lengths.............................................. 123 Figure S11. Summary of distributions of d-Statistic values for the GEA dataset using time- calibrated fossil tips and 3 million-year uniform branch lengths.............................................. 124 Figure S12. Summary of distributions of d-Statistic values for the GEA dataset using time- calibrated fossil tips and 5 million-year uniform branch lengths............................................... 125 Figure S13. Summary of distributions of d-Statistic values for the SEA dataset....................... 126 Figure S14. Correlation between % Missing/non-applicable character scorings (x-axis) and overrepresented/underrepresented fossil squamate skeletal regions........................................... 127 Figure S15. XY scatterplot of the relationship between % Missing/non-applicable character scorings vs. d-statistic values of characters in the Gauthier et al. (2012) dataset....................... 128 Figure S16. XY scatterplot of the relationship between % Missing/non-applicable character scorings vs. d-statistic values of characters in the Simões et al. (2018) dataset......................... 129 Figure S17. Summary of distributions of d-Statistic values for legged taxa from the GEA dataset using time-calibrated fossil tips, 78 calibrated internal nodes from Pyron (2017) and 3 million-year uniform branch lengths................................................................................. 130 Figure S18. Summary of distributions of d-Statistic values for legged taxa from the GEA dataset using time-calibrated fossil tips, 78 calibrated internal nodes from Pyron (2017) and 5 million-year uniform branch lengths....................................................................................... 131 Figure S19. Summary of distributions of d-Statistic values for legged taxa from the GEA dataset using time-calibrated fossil tips, 78 calibrated internal nodes from Pyron (2017) and 7 million-year uniform branch lengths....................................................................................... 132 Figure S20. Summary of distributions of d-Statistic values for the SEA dataset, using only legged taxa.................................................................................................................................. 133 Figure S21. Distributions of d-Statistic for the pruned GEA character dataset using only taxa belonging to Serpentes................................................................................................................ 134 Figure S22. Summary of distributions of d-Statistic values for characters with 0% missing data in the GEA dataset using only limbed squamate taxa......................................................... 135 Figure S23. Summary of distributions of d-Statistic values for characters with 0% missing data in the SEA dataset............................................................................................................... 136 Figure S24. Summary of distributions of d-Statistic values for characters with 0% missing data in the GEA dataset using only limbless squamate taxa....................................................... 137 xv Figure S25. Summary of distributions of d-Statistic values for characters with 0% missing data in the GEA dataset using only taxa included in Serpentes (snakes)................................... 138 Figure S26. Summary of d-Statistic values for characters with 0% missing data, using swapped character matrices and topologies................................................................................ 139 Figure S27. Summary of distributions of d-Statistic values for characters with 0% missing data in the GEA matrix vs. SEA topology dataset, using only limbed squamate taxa and a prior character transition rate of 0.01.......................................................................................... 140 Figure S28. Summary of distributions of d-Statistic values for characters with 0% missing data in the SEA matrix vs. GEA topology dataset, using only limbed squamate taxa and a prior character transition rate of 0.01.......................................................................................... 141 Chapter 5 Figures Figure 1. Visualization of the Character Completeness Metric (CCM2) in the fossil record of non-avian theropod dinosaurs, Mesozoic birds, and squamates................................................. 178 Figure 2. Comparisons of species phylogenetic completeness of non-avian theropod dinosaurs, birds, and squamates preserved in the lacustrine konservat-lagerstätten deposits of the Yixian and Jiufotang formations (Jehol Biota) and the aeolian lagerstätten deposits of the Djadokhta and Baruungoyot formations (Campanian Gobi Desert)..................................... 179 Figure 3. Comparisons of continental-scale differences in the effects of lagerstätten deposits (Djadokhta, Baruungoyot formations; Jehol Biota) on the preservation of phylogenetic character data.............................................................................................................................. 180 Figure 4. Summary of the effects of regional sampling and depositional setting on the amount of available phylogenetic information in the squamate fossil record............................ 182 Figure 5. Summary of distributions of Character Completeness Metric 2 (CCM2) values for squamates found in established lagerstätten localities, with a summary of the number of families represented in localities using the GEA phylogeny...................................................... 183 Supplementary Figures Figure S1. Summary of morphology-based hypotheses of squamate evolutionary relationships, whose character datasets were used for the Character Completeness Metric 2 (CCM2) in this study.................................................................................................................. 189 Figure S2. Distribution of Character Completeness Metric 2 (CCM2) in non-avian theropod dinosaurs from the total Asia dataset (top) and without the 62 surveyed taxa from the Jehol Biota and Campanian Gobi Desert (bottom).............................................................................. 190 xvi Figure S3. Comparisons of squamate families represented in the Gauthier et al. (2012) and Simões et al. (2018) datasets from the Jehol Biota (top) and Campanian Gobi Desert (bottom)....................................................................................................................................... 191 Figure S4. Violin plots of the distribution of non-avian theropod CCM2 values per sampled landmass...................................................................................................................................... 192 Figure S5. Violin plots of the distribution of Mesozoic bird CCM2 values per sampled landmass...................................................................................................................................... 193 Figure S6. Comparisons of distributions of fossil lizard CCM2 values from high- preservation potential depositional environments...................................................................... 194 Figure S7. Comparisons of squamate families represented in the Gauthier et al. (2012) and Simões et al. (2018) datasets from each lagerstätten deposit surveyed in this study.................. 195 Chapter 6 Figures Figure 1. Summary of the flow of anatomical and phylogenetic information in the fossil record, outlined in this dissertation............................................................................................. 249 ABSTRACT xvii While spectacularly-preserved fossils garner the most scientific and public attention, the majority of the world’s fossil collections are comprised of incomplete, fragmentary, and understudied specimens. These collections are treasure troves of paleobiological information, and, in particular, have the potential to be essential data in assessing the evolutionary relationships (i.e., phylogeny) of extinct organisms and their living relatives. Before uncritically incorporating these data into analyses, we must make targeted inquiries into whether the phylogenetic information retained in incomplete fossil specimens is systematically biased in some way. It remains an open question to what degree geological factors, taphonomic factors, and factors related to asymmetrical sampling among workers affect our ability to understand a group’s evolutionary history. In essence, we need to address not just what an imperfect/incomplete fossil record looks like, but also whether it can be trusted within a phylogenetic framework. This study explores these issues using the >242 million-year fossil record of one of the most prominent groups in the modern vertebrate fauna: the Squamata (lizards, snakes, amphisbaenians, mosasaurs, and their relatives). Using: 1) novel applications of an established fossil skeletal completeness metric, as well as: 2) an assessment of skeletal anatomical representation in fossil squamate specimens observed in-person, in electronic collections databases, and the published literature, I aim to quantitatively characterize the geological, taphonomic and anthropogenic sampling biases that contribute to the assembly of a fossil record. I show that the global squamate fossil record, ranging in age from the Middle Triassic to the Late Pleistocene, preserves a highly incomplete amount of phylogenetic information on broad scales. This global pattern is also evident at local and regional levels, which I showcase in a description of new fossil lizard material in the Late Cretaceous of the Western Interior of North America. xviii Anatomical biases are also present in the squamate fossil record, with marginal tooth-bearing bones (i.e., premaxillae, maxillae, dentaries) and vertebrae being overrepresented in global museum collections compared to the rest of the skeleton. Given the incompleteness of the squamate fossil record, it is important to then test a question fundamental to paleobiology: how does incomplete preservation impact the phylogenetic information contained in the fossil record? I test this question by directly measuring the phylogenetic signal (i.e., how well the evolution of a trait aligns with a given evolutionary hypothesis) present in parts of the squamate skeleton that are both overrepresented and underrepresented in the fossil record. Parsimony- and model-based comparative analyses indicate that the most frequently-occurring parts of the squamate skeleton in the fossil record retain similar levels of phylogenetic signal as parts of the skeleton that are rarer. These results demonstrate that the biased squamate fossil record contains reliable phylogenetic information, and support our ability to place incomplete fossils in the Tree of Life. Interrogating the reliability of phylogenetic information preserved in the incomplete squamate record is critical and timely, because our current understanding of squamate evolutionary relationships in Deep Time is filtered heavily through a single place and time. The extraordinarily diverse and complete lizard assemblage from the Campanian Djadokhta and Baruungoyot Formations of Mongolia and China exert an anomalously large influence on patterns of squamate fossil record completeness on global scales, and form a majority of the deep-time structure of squamate evolutionary relationships. As a result, the preservation of phylogenetic information in the global squamate fossil record is particularly susceptible to the “lagerstätten effect” in ways that more completely sampled fossil records, such as that of the non-avian dinosaurs, are not. By incorporating reliable phylogenetic information in incomplete squamate fossil species into xix analyses, we may be able to lessen the “lagerstätten effect” on our understanding of evolutionary relationships. Thus by addressing the taphonomic and sampling biases related to incomplete and exceptionally complete fossils, this study offers a novel phylogenetic framework to interrogate the quality of the fossil record, and introduces methods that can be applied to any fossil group of interest. 1 CHAPTER 1: INTRODUCTION Since Darwin’s time, scientists have lamented the incompleteness of the fossil record (Darwin 1859), and much research has been devoted to characterizing patterns of fossil record bias (e.g., Raup 1979; Smith 1994; Kidwell & Holland 2002). Essentially, the biases present in the fossil record of any given group of organisms lies within three broad spheres of influence (Behrensmeyer et al., 2000): 1) taphonomic biases that filter biological information via the various contributors the processes of fossilization (Behrensmeyer et al., 2000; Sansom et al. 2010); 2) geologic biases that filter biological information via transport, deposition, burial, lithification, rock uplift, weathering, and erosion (Raup 1976; Smith and McGowan 2005); and 3) anthropogenic sampling biases that filter biological information via asymmetrical research interest, taxonomic sampling intensity, and regional sampling intensity (Smith 1994; Smith 2001). While the effects of these biases have been characterized in a growing number of organismal groups (Crane et al. 2004; Mannion & Upchurch 2010; Brocklehurst et al. 2012; Walther & Fröbisch 2013; Brocklehurst & Fröbisch 2014; Cleary et al. 2015; Dean et al. 2016; Verrière et al. 2016; Daviess et al. 2017; Tutin & Butler 2017; Brown et al. 2019; Cashmore & Butler 2019; Driscoll et al. 2019; Lukic-Walther et al. 2019; Mannion et al. 2019; Cashmore et al. 2020), less attention has been paid to whether the phylogenetic information retained in the fossil record is also systematically biased in some way (Sansom et al. 2010). This is a crucial, underexplored problem, because strongly supported phylogenetic relationships are the evolutionary frameworks that synthetic studies of biodiversity (Raup 1979), biostratigraphy (Norell and Novacek 1992), and paleobiogeography (Benson et al. 2013) rely upon (Sakamoto et al. 2017). In this study, I use a novel combination of sampling techniques and phylogenetic 2 comparative methods to quantify the effects of taphonomic, geologic, and anthropogenic sampling biases on phylogenetic information in the fossil record of one of the most prominent groups in the modern vertebrate fauna: the Squamata (lizards, snakes, amphisbaenians, mosasaurs, and their relatives). In Chapter 2, I present a survey of the >242 million-year fossil record of squamates, using a combination of data from the Paleobiology Database (PBDB) and 492 published descriptions of 797 fossil squamate species. I use the well-established Character Completeness Metric (CCM2, Mannion & Upchurch, 2010) to measure the percentage of scoreable phylogenetic characters per fossil squamate species. I then assessed the relationship between the phylogenetic completeness of squamate species and their occurrence in geologic time, their taxonomic affinity, the depositional setting in which they were found, and the region of the world in which they were found. Broadly, results from this survey indicate no meaningful relationship between spatiotemporal sampling intensity and fossil record completeness, but that major differences in squamate fossil record completeness instead stem from a combination of anatomy, body size and affinities of different squamate groups to specific depositional environments. These results reveal novel patterns in the preservation of phylogenetic data on a global scale, and adds crucial contextual data to understanding the evolutionary history of a major component of the modern vertebrate fauna. In Chapter 3, I focus in on a specific region and time period (Late Campanian of North America) and describe new fossil lizard specimens from a poorly-known squamate assemblage in the “Hunter Wash Local Fauna” in the Fruitland and Kirtland Formations in New Mexico. New lizard specimens include: 1) new specimens referable to Chamopsiidae; 2) new material belonging to Scincomorpha, 3) new material belonging to Anguidae; and 4) the first reported 3 predatory lizard (Platynota) material from the Campanian of New Mexico. Although each of these specimens are fragmentary, they nonetheless expand our understanding of Late Cretaceous squamate taxonomy, distribution, and diversity in the Western Interior of North America (a.k.a., Laramidia). Collectively, the described specimens represent family-level diversity similar to that seen in other Campanian foreland basin deposits of the Western Interior, and expand the geographic range of lizard families known from Laramidia. This work represents a significant update to previous erroneous and problematic taxonomic referrals of microvertebrate material in the Fruitland and Kirtland formations, and showcases the importance of filling in critical gaps in the fossil record via field-, and collections-based systematic work. In Chapter 4, I characterize skeletal incompleteness bias in a large dataset (6,585 specimens; 14,417 skeletal elements) of fossil squamates (lizards, snakes, amphisbaenians, and mosasaurs). I show that jaws + palatal bones, vertebrae, and ribs appear more frequently in the fossil record than other parts of the skeleton. This incomplete anatomical representation in the fossil record is biased against regions of the skeleton that contain the majority of morphological phylogenetic characters used to assess squamate evolutionary relationships. Despite this bias, parsimony- and model-based comparative analyses indicate that the most frequently-occurring parts of the skeleton in the fossil record retain similar levels of phylogenetic signal as parts of the skeleton that are rarer. These results demonstrate that the biased squamate fossil record contains reliable phylogenetic information, and support our ability to place incomplete fossils in the Tree of Life. In Chapter 5, I use the CCM2 to quantify the “lagerstätten effect” on the preservation of phylogenetic data in the global fossil record of non-avian theropod dinosaurs, Mesozoic birds, and squamates (e.g., lizards, snakes). In many cases, the fossil record of a given group of 4 organisms is so incomplete that we have to rely heavily on a few exceptionally-preserved fossils from limited geographic areas and narrow slices of geologic time to fill in gaps in our knowledge of a group’s evolutionary history. This widely recognized pattern, known as the “lagerstätten effect”, needs to be characterized and quantified to avoid serious biases in interpretations of the evolutionary relationships of groups of organisms. I show that incomplete fossil records (e.g., Mesozoic birds, squamates) are more susceptible to the “lagerstätten effect” on phylogenetic data, which filters our interpretations of evolutionary relationships through exceptionally preserved taxa in one or two geologic units. Unexpectedly, the results herein indicate that the aeolian deposits of the Late Cretaceous Gobi Desert of Mongolia and China preserve exceptionally complete lizard anatomical and phylogenetic data, such that those deposits exert an anomalously large influence on patterns of squamate fossil record completeness on global scales, and the deep-time structure of squamate evolutionary relationships. These findings from aeolian- dominant facies demonstrate that the potential to preserve a high quantity and quality of evolutionary information is not necessarily restricted to traditional lagerstätten. Quantifying formation-specific preservation of phylogenetic information in multiple groups offers a novel comparative lens through which to assess the effects of exceptionally preserved fossil assemblages on our interpretations of the Tree of Life. References Behrensmeyer, A. K., S. M. Kidwell, and R. A. Gastaldo. 2000. Taphonomy and paleobiology. Paleobiology 26(S4):103-147. Brocklehurst, N., and J. Fröbisch. 2014. Current and historical perspectives on the completeness of the fossil record of pelycosaurian-grade synapsids. Palaeogeography, Palaeoclimatology, Palaeoecology 399:114-126. Brocklehurst, N., P. Upchurch, P. D. Mannion, and J. O'Connor. 2012. The completeness of the fossil record of Mesozoic birds: implications for early avian evolution. PLoS One 7(6):e39056. 5 Brown, E. E., D. D. Cashmore, N. B. Simmons, and R. J. Butler. 2019. Quantifying the completeness of the bat fossil record. Palaeontology 62(5):757-776. Cashmore, D. D., and R. J. Butler. 2019. Skeletal completeness of the non‐avian theropod dinosaur fossil record. Palaeontology 62(6):951-981. Cashmore, D. D., P. D. Mannion, P. Upchurch, and R. J. Butler. 2020. Ten more years of discovery: revisiting the quality of the sauropodomorph dinosaur fossil record. Palaeontology 63(6):951- 978. Cleary, T. J., B. C. Moon, A. M. Dunhill, and M. J. Benton. 2015. The fossil record of ichthyosaurs, completeness metrics and sampling biases. Palaeontology 58(3):521-536. Crane, P. R., P. Herendeen, and E. M. Friis. 2004. Fossils and plant phylogeny. American Journal of Botany 91(10):1683-1699. Darwin, C. R. 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, London. Davies, T. W., M. A. Bell, A. Goswami, and T. J. Halliday. 2017. Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction. Paleobiology 43(4):521-536. Dean, C. D., P. D. Mannion, and R. J. Butler. 2016. Preservational bias controls the fossil record of pterosaurs. Palaeontology 59(2):225-247. Driscoll, D. A., A. M. Dunhill, T. L. Stubbs, and M. J. Benton. 2019. The mosasaur fossil record through the lens of fossil completeness. Palaeontology 62(1):51-75. Kidwell, S. M., and S. M. Holland. 2002. The quality of the fossil record: implications for evolutionary analyses. Annual Review of Ecology and Systematics 33(1):561-588. Lukic-Walther, M., N. Brocklehurst, C. F. Kammerer, and J. Fröbisch. 2019. Diversity patterns of nonmammalian cynodonts (Synapsida, Therapsida) and the impact of taxonomic practice and research history on diversity estimates. Paleobiology 45(1):56-69. Mannion, P. D., A. A. Chiarenza, P. L. Godoy, and Y. N. Cheah. 2019. Spatiotemporal sampling patterns in the 230 million year fossil record of terrestrial crocodylomorphs and their impact on diversity. Palaeontology 62(4):615-637. Mannion, P. D., and P. Upchurch. 2010. Completeness metrics and the quality of the sauropodomorph fossil record through geological and historical time. Paleobiology 36(2):283-302. 6 Raup, D. M. 1976. Species diversity in the Phanerozoic: an interpretation. Paleobiology:289-297. Raup, D. M. 1979. Biases in the fossil record of species and genera. Bulletin of the Carnegie Museum of Natural History 13:85-91. Sansom, R. S., S. E. Gabbott, and M. A. Purnell. 2010. Non-random decay of chordate characters causes bias in fossil interpretation. Nature 463(7282):797-800. Smith, A. B. 1994. Systematics and the Fossil Record. Documenting Evolutionary Patterns. Blackwell Scientific Publications, London. Smith, A. B. 2001. Large–scale heterogeneity of the fossil record: implications for Phanerozoic biodiversity studies. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 356(1407):351-367. Smith, A. B., and A. J. McGowan. 2005. Cyclicity in the fossil record mirrors rock outcrop area. Biology Letters 1(4):443-445. Tutin, S. L., and R. J. Butler. 2017. The completeness of the fossil record of plesiosaurs, marine reptiles from the Mesozoic. Acta Palaeontologica Polonica 62(3):563. Verrière, A., N. Brocklehurst, and J. Fröbisch. 2016. Assessing the completeness of the fossil record: comparison of different methods applied to parareptilian tetrapods (Vertebrata: Sauropsida). Paleobiology 42(4):680-695. Walther, M., and J. Fröbisch. 2013. The quality of the fossil record of anomodonts (Synapsida, Therapsida). Comptes Rendus Palevol 12(7-8):495-504. 7 CHAPTER 2: THE PRESERVATION OF PHYLOGENETIC INFORMATION IN THE GLOBAL SQUAMATE FOSSIL RECORD Abstract Fossil data is subject to inherent biological, geological, and anthropogenic filters that can distort our interpretation of evolutionary relationships of organisms in deep time. The inevitable presence of incomplete fossils require a holistic assessment of how to navigate the downstream effects of bias on our ability to accurately reconstruct evolutionary relationships, which are essential to analyses of diversification, paleobiogeography, and biostratigraphy in Earth history. In this study, I use an established completeness metric to quantify the effects of geological, taphonomic and sampling biases on the amount of phylogenetic information available in the fossil record of squamates (lizards, snakes, amphisbaenians, and mosasaurs). I use published descriptions of 797 fossil squamate species and 16,983 corresponding specimens spanning 242 million years of the group’s evolutionary history. This study found no meaningful relationship between spatiotemporal sampling intensity and fossil record completeness, but that major differences in squamate fossil record completeness stem from a combination of anatomy/body size and affinities of different squamate groups to specific depositional environments. These results reveal novel patterns in the preservation of phylogenetic data on a global scale, and add crucial contextual data to understanding the evolutionary history of a major component of the modern vertebrate fauna. 8 2.1. Introduction Any effort to reconstruct biodiversity in Earth’s geologic past hinges on the ability to characterize and quantify the downstream effects of bias in the fossil record. Fossil data, from a cellular to a global level, is subject to various geological filters (Raup 1976; Smith & McGowan 2005), taphonomic filters (Sansom et al. 2010), and sampling filters (Smith 1994, 2001), that distort our understanding of ancient life. If left unaccounted for, these biases represent significant barriers to paleobiological inquiry (Kidwell & Holland, 2002) that can obscure the myriad of anatomical, ecological, and evolutionary signals contained in the rock record. Although the incompleteness of fossil data is an established reality in paleobiology (Darwin 1859; Foote & Sepkoski 1999; Smith, 2001; Kidwell & Holland 2002; Woolley et al. 2022), a growing number of studies have employed a variety of novel metrics to characterize and quantify fossil record biases in organismal groups (Crane et al. 2004; Mannion & Upchurch 2010; Brocklehurst et al. 2012; Walther & Fröbisch 2013; Brocklehurst & Fröbisch 2014; Cleary et al. 2015; Dean et al. 2016; Verrière et al. 2016; Daviess et al. 2017; Tutin & Butler 2017; Brown et al. 2019; Cashmore & Butler 2019; Driscoll et al. 2019; Lukic-Walther et al. 2019; Mannion et al. 2019; Cashmore et al. 2020). Combined with an increasing number of sampling proxies to account for a multitude of biases in paleobiological data (Darroch & Saupe 2018; Darroch, Fraser & Casey 2021; Darroch et al. 2022, Lukic-Walther et al., 2019), we are equipped with an advanced toolkit to explore outstanding questions related to biodiversity in the fossil record. However, the association between fossil record incompleteness and our ability to infer evolutionary relationships of fossil organisms remains a pressing, but underexplored question (Sansom et al. 2010, 2017; Sansom 2015; Brocklehurst & Benevento 2020; Woolley et al., 2022). 9 Using established “completeness metrics” for a fossil record is one of the most straightforward ways to assess potential barriers to reconstructing the evolutionary relationships (i.e., phylogeny) of extinct organisms. In this study, I use the Character Completeness Metric (CCM; Mannion & Upchurch, 2010), to measure the percentage of phylogenetic characters that can be scored for a given fossil species, based on the preserved elements of a species’ anatomy. The CCM is extremely useful in quantifying both the physical completeness of the fossil record of organismal groups, but also quantifies potential barriers to reconstructing their evolutionary relationships, which are essential to the frameworks that synthetic studies of biodiversity (Raup, 1979), biostratigraphy (Norell & Novacek 1992), and paleobiogeography (Benson et al. 2013) rely upon. I use the CCM to quantify the completeness of the fossil record of squamates (lizards, snakes, amphisbaenians, and mosasaurs), a group that has both an extensive fossil record stretching back at least 242 million years (Simões et al. 2018), and is major component of the modern vertebrate fauna (>11,349 extant species, Uetz et al. 2022). I identify and test for differences in anatomical, geological, and collecting biases that lead to the distribution of phylogenetic data of 797 fossil squamate species (16,983 assigned specimens) throughout their evolutionary history. By characterizing the downstream effects of bias within the squamate fossil record, we can better navigate through geological, taphonomic and anthropogenic obstacles to reconstructing true biodiversity patterns in Earth’s past. 2.2. Materials & Methods 2.2.1 Sampling the published squamate fossil record General taxonomic, stratigraphic and occurrence-based data from the published fossil record of lizards, snakes, mosasaurs and amphisbaenians was downloaded from the Paleobiology 10 Database (PBDB; Data downloaded June 5 th , 2020 using the following criteria: Order: Squamata). I limited my data to the species level, as both phylogenetic datasets used in this study (Gauthier et al. 2012 [GEA]; Simões et al. 2018 [SEA]) use species as their operational taxonomic units. I also excluded extant species found in the squamate fossil record, as each extant species included in the GEA and SEA phylogenetic datasets was based on modern morphological and molecular data. In total, I sampled the published record of 797 species and 16,983 specimens of extinct squamates, that range from the Middle Triassic (Anisian) to the late Pleistocene in age. PBDB information for each fossil species was vetted using published specimen and locality descriptions (See Supplementary Data and Chapter 5 for an extended list of references). 2.2.2. Fossil completeness metric and phylogenetic datasets To assess the completeness of the global fossil record of lizards, snakes, mosasaurians and amphisbaenians, I used the Character Completeness Metric 2 (CCM2, Mannion & Upchurch 2010), which measures the percentage of appropriate phylogenetic characters that can be scored for all specimens referred to a fossil species. I used two morphological character datasets that represent the two major morphology-based hypotheses of squamate evolutionary relationships (GEA and SEA, Figure 1). I combined these two datasets and removed overlapping characters. Individual species’ completeness were scored based on the presence of individual skeletal elements for which a corresponding portion of the combined phylogenetic characters could be scored. I carried out scoring CCM2 percentages under two categories: 1) Raw Completeness, in which a species’ CCM2 percentage was scored out of all 860 phylogenetic characters available in the combined GEA + SEA dataset; 2) True Completeness, in which a species’ CCM2 percentage was scored only from the characters that the species could be scored for. For instance, 11 many fossil snake and amphisbaenian species do not possess limbs. This means that, no matter how complete the skeletal remains are, snake and amphisbaenian species would always be missing 150 characters that correspond to the limbs and limb girdles. Because of this disparity, I also measured legless squamate taxa’s “True Completeness” scored out of 710 characters instead of 860. (Supplementary data). 2.2.3. Data visualization and statistical tests All data visualization and statistical tests were carried out in R (R Core Team, 2013). Time series plots were visualized using the geoscale package in R (Bell, 2022). The mean, standard deviation, and median of CCM2 scores for all species occurring within a geological time bin were calculated to detect fluctuations of the quality of the squamate fossil record though time. Violin plots of various partitions of non-temporal range data were visualized using the vioplot package in R (Adler et al., 2021). Linear regression analysis was carried out for linear time series comparisons with the functions lm() in the stats package in R. Generalized least squares regressions (GLS) was performed using the function gls() in the R package nlme (Pinheiro et al. 2018), in which a first order autoregressive model (cor-AR1) is applied to the data, to avoid overestimating statistical significance due to temporal autocorrelation. I carried out analyses using both raw values and with log-transformed values to ensure homoscedasticity (constant variance) and normality of residuals. The function r.squaredLR() of the R package MuMIn (Bartón 2019) was also used to calculate likelihood-ratio based pseudo-R2 values. Nonparametric pairwise statistical comparisons of non-temporal range CCM2 data were carried out using the Mann-Whitney U-Test and the Kolmogorov-Smirnov Test. Because I performed multiple statistical comparisons among both landmasses and among depositional environments, statistical tests were run using a Bonferroni correction on the α value. 12 2.3. Results 2.3.1. The completeness of the squamate fossil record through geologic time The time series data for sampled species of extinct squamates through time is summarized in Figure 2A. The squamate fossil record for the Triassic and Jurassic includes 10 out of 16 stage bins that do not contain a published record of a fossil referable to a squamate species. Three of the remaining 6 stages contain only one sampled published squamate species (Anisian, Toarcian, Oxfordian), and the maximum number of published squamate fossils referable to a species in a given stage is 6 (Tithonian). These results illustrate a discontinuous and poorly sampled record of squamates during the early stages of their evolutionary history. However, from the Late Jurassic through Late Pleistocene, the squamate fossil record is substantially more continuous, with only one major stage (Salandian; middle Paleocene) without a published fossil referable to a squamate species. Only one stage (Coniacian) contains a single species, while 5 stages contain >50 species (Campanian, 111; Maastrichtian, 70; Ypresian, 112; Priabonian, 61; Burdigalan, 51). 569 out of the 797 sampled extinct squamate species are found in stages occurring either in the Late Cretaceous or the Paleogene. With the exception of the Burdigalan (early Miocene), the number of sampled extinct squamates per stage generally decreases from the end of the Eocene toward the present. Figure 2B illustrates the number of published specimens (with catalogue numbers and/or quantifications) assigned to the sampled squamate species in this study. Although there is sometimes considerable variation between peaks and troughs on the curve, particularly in the Miocene, there is a general increase in the number of specimens assigned to extinct squamate species from the beginning of their evolutionary history toward the present. Some published descriptions include only a single specimen (e.g., Hongshangxi xei, Dong et al., 2019), while 13 other descriptions include thousands (e.g., Coluber hungaricus, Venczel 1994, 1998). However, with only two major exceptions (the Burdigalan and Messinian in the Miocene), the abundance of specimens during a given geological stage correlates strongly with the number of species (R 2 = 0.6997, Supplementary Data). I plotted each species’ CCM2 percentage in their corresponding geologic stage (gray dots, Fig. 2C), and overlaid those scores trendlines indicating the mean and median CCM2, as well as the standard deviation (1s) for CCM2 values. The mean CCM2 percentage of extinct squamates showcases considerable variation in the patchy and less-well sampled Triassic and Jurassic, whereas the major peaks in mean CCM2 percentage in the much more thoroughly- sampled Cretaceous appear to be driven by lagerstätten-type deposits, such as the Yixian (China) and Las Hoyas (Spain) lacustrine deposits (Barremian-Aptian) and the Djadokhta and Baruungoyot aeolian deposits (Mongolia) and Smoky Hill Chalk (United States) marine deposits (Campanian). The Cenozoic record of squamates includes ~60% of all surveyed extinct squamate species, but despite the heavier sampling and the presence of many highly complete squamates from lacustrine lagerstätten deposits such as the Green River Formation (United States) and Messel (Germany), the mean CCM2 per stage rarely reaches the heights nor the variation observed during the Mesozoic. Only the seven squamate species in the Messinian (late Miocene) Cave deposits in Hungary (Bolkay, 1913; Venczel, 1994, 1998) allow for a mean CCM2 to reach comparable levels to those seen in the Mesozoic. The standard deviation of CCM2 values tracks the variation seen in the Mean CCM2 through time, but also on average gradually decreases toward the present. The Median CCM2 through time skews lower than the mean, especially when the numerous but highly incomplete fossil snake species become prevalent in the fossil record in the Maastrichtian up to the present. Simple linear regression analyses show no 14 statistically significant correlation between the number of species sampled and their corresponding completeness. However, there is a statistically significant weak positive relationship between the number of specimens assigned to a given species and its corresponding completeness (p= 0.00077; adjusted R 2 = 0.131 Supplementary Data). My GLS analyses investigated the relationship between sampled species and mean CCM2 percentage per time bin and sampled specimens and mean CCM2 percentage per time bin. For both comparisons only using non-transformed values, the autoregressive model had a higher R-squared value (CCM2~Species: 0.409; CCM2~Specimens; 0.438), but the model fit was not statistically significant (All p-values > 0.05, Supplementary Data). When I log- transformed the data for both comparisons, I found weak positive relationships (CCM2~Species: 0.176; CCM2~Specimens; 0.190), that are not statistically significant (All p-values > 0.05, Supplementary Data). I also parsed out completeness through time among major squamate groups and body plans (lizards, snakes, Mosasauria, and amphisbaenians, Fig. 2D). Here, we observe patterns in fossil record completeness and continuity through time that illustrate the disparities of fossil preservation among members of the same group of organisms. The fossil record of lizards spans the longest amount of geologic time, but includes significant gaps in sampling the Triassic, Jurassic, and Neogene. The gaps in the Neogene are most likely driven by the assignment of a fossil specimen to an extant species of lizard. Because extant species were not included in my sampling of the fossil record, these gaps are an artefact of my own sampling in this study, rather than a reflection of true gaps in the presence of lizards in the fossil record. Lizard mean CCM2 consistently hovers between 20% and 40% through geologic time, with the exceptions of stages with low numbers (n<6) of taxa in the Triassic and Jurassic, and the lacustrine lagerstätten- 15 driven peak in the Barremian. Fossil snakes span the second-longest amount of geologic time, but their mean completeness consistently hovers between 5% and 20% – much lower on average than that of their lizard counterparts. Mosasaurs, the extinct clade of giant marine squamates spanning in age from the Aptian to the Maastrichtian, exhibit higher mean CCM2 in most geologic stages than lizards and snakes. Finally, amphisbaenians, which range in age from the Early Paleogene to the present, exhibit higher mean CCM2 scores than their lizard and snake counterparts in most stages in which their fossils are found. 2.3.2. Taxonomic comparisons I carried out pairwise statistical comparisons between median CCM2 percentages (Mann- Whitney U) and cumulative distribution (Kolmogorov-Smirnov) of CCM2 percentages in the fossil record of lizards, snakes, mosasaurs and amphisbaenians (Figure 3A). Results from these tests indicate that the fossil record of each taxonomic group has a statistically significantly different median CCM2 percentage (only exception: Mosasauria compared with Amphisbaenians p = 0.1734) and has a statistically significantly different distribution of CCM2 percentages (All p-values < 0.05, Supplementary Data). Mosasaurs exhibit the highest median CCM2 percentage (39.25%), followed by amphisbaenians (18.87%), lizards (13.59%), and snakes (4.79%) (Figure 3A). 2.3.3. Regional sampling comparisons The left panel of Figure 4 displays the distribution of CCM2 percentages for 10 landmasses in order of increasing sample size of fossil squamate species. Antarctica and the Caribbean have low sample sizes (n = 2 and n = 3, respectively), and I attribute their high median CCM2 values and odd distributions to a sampling artifact. As we increase sample size from n = 6 (Madagascar) to n = 283 (North America), we observe that the maximum CCM2 16 value increases with sample size. Pairwise statistical comparisons between median CCM2 percentages (Mann-Whitney U) and cumulative distribution (Kolmogorov-Smirnov) among landmasses show no statistically significant differences among most landmasses, with only one notable exception in the data obtained from Asia. For this landmass, the median CCM2 percentage and the cumulative distribution shape of fossil squamate species are statistically significantly different from all other landmasses, with the exception of the three landmasses with the lowest sample sizes (Antarctica, Caribbean, Madagascar) and Australasia. A minor exception to this overall lack of difference is that the median CCM2 percentage of Australasia and India are statistically significantly different. 2.3.4. Depositional setting and completeness Pie charts illustrating the relative abundance of fossil squamate species found in depositional environments are shown on the right hand side of the violin plots of the CCM2 distributions for landmasses in Figure 4. The distribution of CCM2 values per depositional environment with 17 or more sampled fossil squamate species are shown on the right hand panel of Figure 4. Pairwise statistical comparisons between median CCM2 percentages (Mann- Whitney U) and cumulative distribution (Kolmogorov-Smirnov) among these distributions reveal a several patterns. First and foremost, the median and distribution shape of CCM2 percentages from Aeolian environments is statistically significantly different from every other surveyed environment apart from the median marine CCM2 value. Second, the median and distribution shape of the CCM2 values from lacustrine environments differ from those seen in fluvial channel and karst environments. Third, the median and distribution shape of CCM2 values in karst environments also differs from those of marine and coastal lagoon depositional settings. Lastly, the median and distribution shape of CCM2 values in marine depositional 17 environments are statistically significantly different from those found in all three fluvial depositional categories (fluvial floodplain, fluvial channel, fluvial indet.). I also examined the distribution of different groups of squamates across all depositional environments in our survey (Figure 5). For each squamate group (lizards, snakes, mosasaurs, and amphisbaenians, Fig. 5A-D), I removed species that did not include sufficient lithology/locality information in their descriptions (i.e., terrestrial indet.) and focused on the distribution of species found in specific enough depositional environments (Fig. 5E-H). For each group, the relative abundance of depositional environments differs. The three largest proportions of species of fossil lizard are found in fluvial, lacustrine, and aeolian environments (Fig. 5E). Unsurprisingly, the vast majority of mosasaurians are found in marine/nearshore depositional environments (Fig. 5F). The three largest proportions of species of fossil snake are found in fluvial, karstic/cave environments and marine/nearshore settings (Fig 5G). Close to half of the sampled fossil amphisbaenians are found in fluvial settings, while three have been found in volcaniclastic environments and two have been found in lacustrine and karstic environments (Fig. 5H). In considering the mean CCM2 value per group per depositional environment (Fig. 5I), we observe that: 1) mosasaurians exhibit relatively high mean CCM2 in all depositional environments they are found in; 2) snake fossils are found in most depositional environments, but their mean CCM2 score remains mostly below 10% for most settings; 3) fossil lizards are much more complete in proximal depositional settings (alluvial fans; volcaniclastic, aeolian, lacustrine) than distal/nearshore/marine environments; 4) amphisbaenians exhibit higher mean CCM2 values in fluvial environments than the other three groups. 18 2.4. Discussion 2.4.1. Phylogenetic completeness patterns through geologic time My linear and generalized least-squares regression analyses find no significant correlation between mean CCM2 and the number of species per sampled geologic time bin. These results are consistent with recent studies assessing character completeness in the fossil record of a variety of vertebrate groups (e.g., Mannion & Upchurch, 2010; Brocklehurst & Fröbisch, 2014; Lukic-Walter et al., 2019; Brown et al., 2019; Mannion et al. 2019). Although I do not employ any diversity estimates herein, these results suggest, at the very least, that taxonomic richness of squamates in a given time bin does not predict the amount of phylogenetic data available. In all three regression analyses, the number of sampled specimens better predicted the mean completeness in a time interval, but R 2 values are still low and only the linear regression results were statistically significant (Supplementary Data). The lack of any strong correlation between number of specimens sampled and completeness shows that increasing specimen sampling is not necessarily a reliable indicator of completeness, but it is observably better than using taxonomic richness. In all, these time series results suggest that increases or decreases in temporal sampling intensity do not correlate with the amount of available phylogenetic data through geologic time. 2.4.2. Effects of taxonomy/body plan on phylogenetic completeness Each of the four taxonomic/body plan groups I included in this survey (lizards, snakes, mosasaurs, and amphisbaenians) have statistically significant distributions of available phylogenetic data in their fossil records (Figure 3A, Supplementary Data). This highlights the extreme morphological disparity within squamates, and how that disparity lends itself to vastly different preservation of phylogenetic information. While previous studies have compared the 19 CCM2 distributions of morphologically distinct groups of tetrapods (e.g., birds and sauropodomorph dinosaurs, Brocklehurst et al. 2012; bats and a slew of other tetrapod groups, Brown et al. 2019), the distributions of CCM2 values for each group are not drawn from the same set of phylogenetic characters, and could influence how meaningful the comparisons between, say, body size and completeness might be. The distributions of CCM2 values in this study are drawn from the same set of phylogenetic characters, and therefore allows for meaningful comparison between different body plans. It is not surprising that mosasaurs have a statistically significantly different median CCM2 and distribution shape than other squamate groups in this survey. Larger body size generally lends itself well to likelihood of preservation, and, anecdotally, larger fossilized bones are easier to pick out with the naked eye when surveying rock outcrop for fossils. Therefore, the fact that mosasaurs have the highest median completeness value is not unexpected. Fossil lizards unsurprisingly have a statistically significantly different median CCM2 value and distribution shape because they do not generally possess the size of their mosasaur counterparts, nor do they generally possess the limbless condition seen in snakes and amphisbaenians (very few of the sampled fossil lizard species preserve evidence of the limb-reduced/limbless condition). The difference between fossil snakes and fossil amphisbaenians is striking because they are groups dominated by legless taxa with elongate bodies and some overlapping ecology. However, a major explanation for the much higher median CCM2 value for amphisbaenians could lie in their skull anatomy. Amphisbaenians possess highly modified skulls for borrowing, such that many bones are fused together to form a hardened surface useful in digging through substrate. This fusion of the skull increases its preservation potential, and this is borne out in the substantial representation of the skull in the fossil record of amphisbaenians. Because the skull is 20 such a phylogenetic character-dense region, the fossil record of amphisbaenians, with their increased preservation potential of the skull, is significantly more complete than the record of snakes. Because snakes have delicate skulls, their record is mostly confined to the least character-dense region of the squamate skeleton: vertebrae. As a result, even though snakes and amphisbaenians largely share the same type body plan, their respective skull anatomy is a major driver of the differences observed. 2.4.3. Effects of regional sampling biases on phylogenetic completeness Statistical comparisons among sampling of landmasses were inconclusive, with the exception of the median and distribution shape of fossil squamate species found in Asia (Fig. 4, left panel). The cause for this discrepancy is almost certainly due to the presence of 50 highly phylogenetically complete lizard taxa sampled from the Late Campanian Djadokhta and Baruungoyot aeolian deposits in Mongolia and China. Indeed, if these taxa are removed, the distribution shape and median value do not showcase any statistically significant differences from the rest of the sampled landmasses (See Chapter 5). The lack of statistically significant differences in completeness among different regions suggests that regional sampling intensity does not alter the overall distribution of available phylogenetic information. However, these data shows that increased sampling intensity correlates with our ability to uncover the most complete fossils. This suggests that the same taphonomic and sampling filters apply to our understanding of the fossil record regardless of sampling region, but the landmasses with the most sampled species also happen to be the landmasses with the most complete squamate fossils. The results for squamates are largely consistent with patterns observed in other global datasets (e.g., Mannion & Upchurch, 2010; Brocklehurst et al. 2012). 21 2.4.4. Effects of depositional environment on phylogenetic completeness The major differences in phylogenetic completeness of the squamate fossil record among different depositional environments are largely dependent on the type of taxon that dominates the environment. The three environments that showcased the most statistically significant differences in median CCM2 values and CCM2 distribution shape are marine environments, karst environments, and aeolian environments (Figure 4, right panel). The majority of sampled squamate species that are found in marine environments are highly complete mosasaurs (69 out of 86 species) driving both the median CCM2 value higher and skewing the distribution higher. In karst depositional environments, the majority of sampled squamate species are highly incomplete snakes (32 out of 52 species), driving the median CCM2 value lower and skewing the distribution toward lower values. A large number of highly complete lizard species are represented in aeolian depositional environments (52 out of 52 species), leading to the highest observed median CCM2 value among depositional environments and to a CCM2 distribution shape that is extremely different from any other observed depositional environment. Taken together, taxonomic affinities with these three specific depositional environments could be a leading cause behind the significant differences in distribution of phylogenetic data. Another observed statistically significant difference is in the distribution of CCM2 scores between low-energy, hypersaline/anoxic depositional environments (lacustrine, coastal lagoon) and high-energy fluvial channel environments. These differences are better explained by geological factors than by skewed taxonomic affinity. Both lizards and snakes are found in abundance in all three of these depositional settings, and therefore any differences cannot be attributed to an overrepresentation of one group over another. Coastal lagoon and lacustrine depositional settings preserve more complete lizard and snake fossils (lagoon lizards mean 22 CCM2 = 31.8%; lagoon snakes mean CCM2 = 23.7%; lacustrine lizards mean CCM2 = 38.0%; lacustrine snakes mean CCM2 = 19.8%) than in fluvial channel settings (fluvial channel lizards mean CCM2 = 20.6%). These results are consistent with previous generalized observations about the quality of the fossil record of lizards and snakes (Nydam, 2013, Rage 2013), in that taxa found in fluvial settings tend to be highly incomplete compared to their lagoon/lacustrine counterparts. 2.5. Conclusion Understanding temporal, spatial, geological, and anatomical biases that contribute to nature of the fossil record is crucial to reconstructing biodiversity in the recent and distant past. In describing patterns in the completeness of the fossil record of squamates, I have been able to quantify the effects of sampling intensity, geological bias, and anatomical biases on our ability to reconstruct the phylogeny of extinct members of a massive component of the modern fauna. Although the fossil record of squamates overall is not a portrait of exceptional preservation, there are distinctive patterns within their record in differing depositional environments and their anatomy that contribute to a more synergistic understanding of their evolutionary history. In describing these patterns, I found that understanding the anatomical biases that lead to different proportions of phylogenetic information in the fossil record can help parameterize gaps in knowledge of the fossil record, and invite us to prioritize those gaps in future sampling endeavors. 23 References Adler, D., Kelly, S.T., Elliott, T.M. 2021. Package ‘vioplot’. Available online : < https://cran.r- project.org/web/packages/vioplot/vioplot.pdf>. Accessed November 2021. Bailon, S. 2000. Amphibiens et reptiles du Pliocène terminal d’Ahl al Oughlam (Casablanca, Maroc). Geodiversitas 22(4):539-558. Bartón, K. 2019. Package ‘MuMIn’. 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Dental data perform relatively poorly in reconstructing mammal phylogenies: morphological partitions evaluated with molecular benchmarks. Systematic Biology 66(5):813-822. Simões, T. R., M. W. Caldwell, M. Tałanda, M. Bernardi, A. Palci, O. Vernygora, F. Bernardini, L. Mancini, and R. L. Nydam. 2018. The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps. Nature 557(7707):706-709. 26 Smith, A. B. 1994. Systematics and the Fossil Record. Documenting Evolutionary Patterns. Blackwell Scientific Publications, London. Smith, A. B. 2001. Large–scale heterogeneity of the fossil record: implications for Phanerozoic biodiversity studies. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 356(1407):351-367. Smith, A. B., and A. J. McGowan. 2005. Cyclicity in the fossil record mirrors rock outcrop area. Biology Letters 1(4):443-445. Tutin, S. L., and R. J. Butler. 2017. The completeness of the fossil record of plesiosaurs, marine reptiles from the Mesozoic. Acta Palaeontologica Polonica 62(3):563. Uetz, P. F., Paul; Aguilar, R; Hošek, Jirí. 2021. The Reptile Database. http://www.reptile-database.org. Venczel, M. 1994. Late Miocene snakes from Polgárdi (Hungary). Acta Zoologica Cracoviensia 37(1):1-29. Venczel, M. 1998. Late Miocene snakes [Reptilia: Serpentes] from Polgardi [Hungary]: a second contribution. Acta Zoologica Cracoviensia 41(1). Verrière, A., N. Brocklehurst, and J. Fröbisch. 2016. Assessing the completeness of the fossil record: comparison of different methods applied to parareptilian tetrapods (Vertebrata: Sauropsida). Paleobiology 42(4):680-695. Walther, M., and J. Fröbisch. 2013. The quality of the fossil record of anomodonts (Synapsida, Therapsida). Comptes Rendus Palevol 12(7-8):495-504. Woolley, C. H., J. R. Thompson, Y.-H. Wu, D. J. Bottjer, and N. D. Smith. 2022. A biased fossil record can preserve reliable phylogenetic signal. Paleobiology 48(3):480-495. 27 Figures Figure 1. Summary of morphology-based hypotheses of squamate evolutionary relationships, whose character datasets were used for the Character Completeness Metric 2 (CCM2) in this study. A) Gauthier et al. (2012) hypothesis. B) Simões et al. (2018) hypothesis. Silhouettes indicate major squamate groups whose phylogenetic positions differ among the two hypotheses. All silhouettes traced from publicly available images at www.phylopic.org. 28 Figure 2. Time series plots of fossil squamate data used in this study. A) Sampled extinct squamate species through time. B) Sampled specimens assigned to extinct squamate species through time. C) Mean (sky blue line), standard deviation (blue shading) and median (red line) Character Completeness Metric 2 (CCM2) percentages of all sampled squamate species through time. Gray dots indicate CCM2 scores of individual species within each time bin. D) Separated mean CCM2 percentages for lizards (purple) snakes (orange), mosasaurs (green) and amphisbaenians (aqua) through time. 29 Figure 3. Summary of Character Completeness Metric 2 (CCM2) distributions among squamate taxonomic groups and line drawings of representative examples of various completeness percentages. A) Violin plots of CCM2 distributions for lizards (purple), snakes (orange), mosasaurs (green) and amphisbaenians (aqua). White dot: median; black bar: interquartile range; black line: 95% confidence interval. B) Example of a fossil lizard species with a CCM2 percentage of roughly 25% (Asagaolacerta tricuspidens, Evans & Matsumoto 2015). C) Example of a fossil lizard species with a CCM2 percentage of roughly 50% (Heloderma texana, Stevens 1977). D) Example of a fossil lizard species with a CCM2 percentage of roughly 75% (Saichangurvel davidsoni, Conrad & Norell 2007). E) Line drawing of fossil squamate species with the highest observed CCM2 percentage (Saniwa ensidens, Rieppel & Grande 2007). F) Line drawing of fossil squamate species with the lowest observed CCM2 percentage (Anolis electrum, Lazell 1965). 30 Figure 4. Violin plots of the distribution of squamate Character Completeness Metric 2 (CCM2) percentages per landmass (left) and per depositional setting (right). White dot: median; black bar: interquartile range; black line: 95% confidence interval. Pie charts show the relative proportions of depositional environments in which fossil lizard, snake, mosasaur and amphisbaenian species are found per corresponding landmass. 31 Figure 5. Summary of affinities between fossil lizard, snake, and amphisbaenian Character Completeness Metric 2 (CCM2) distributions and depositional environment. Species without specific lithological descriptions from their respective localities (i.e., terrestrial indet.) are excluded. A) Distribution of CCM2 scores for fossil lizard species. Center of panel: line drawing of the holotype specimen of Asprosaurus bibrongriensis (KDRC-BB4, associated skull, jaw, axial, and appendicular elements, Park, Evans & Huh 2015), representing the median CCM2 score of 20.91%. B) Distribution of CCM2 scores for fossil mosasaur species. Center of panel: line drawing of the holotype specimen of Taniwhasaurusi oweni (KHM N99-1014/1-5, Caldwell et al., 2005), representing a median CCM2 score of 39.26%. C) Distribution of CCM2 scores for fossil snake species. Center of panel: line drawing of the holotype specimen of Thaumastophis missiaeni (VAS 1017, an isolated trunk vertebra, Rage et al. 2008), representing the median CCM2 score of 3.94%. D) Distribution of CCM2 scores for fossil amphisbaenian species. Center of panel: line drawing of the holotype specimen of Trogonophis darelbeidae (composite of AaO 2117-2120, Bailon, 2000), representing the median CCM2 score of 18.45%. E-H) Pie charts illustrating the relative distribution of depositional settings containing surveyed fossil lizard (E), mosasaur (F), snake (G), and amphisbaenian (H) species. Color codes for each environment are presented in (I). I) Plot illustrating mean CCM2 scores per depositional environment for fossil lizards (purple), mosasaurs (green), snakes (orange), and amphisbaenians (aqua). 32 CHAPTER 3. NEW FOSSIL LIZARD SPECIMENS FROM A POORLY-KNOWN SQUAMATE ASSEMBLAGE IN THE LATE CRETACEOUS (CAMPANIAN) SAN JUAN BASIN, NEW MEXICO, USA This paper was published as: Woolley, C. H., N. D. Smith, and J. J. Sertich. 2020. New fossil lizard specimens from a poorly-known squamate assemblage in the Upper Cretaceous (Campanian) San Juan Basin, New Mexico, USA. PeerJ 8:e8846. Abstract Recent collection efforts in the upper Campanian (~76-73.5 Ma) Fruitland and Kirtland formations of northwestern New Mexico have significantly increased the taxonomic diversity of lizards in this historically poorly understood squamate assemblage. New lizard specimens from the “Hunter Wash Local Fauna” of the upper Fruitland and lower Kirtland formations include: (1) new specimens referable to Chamopsiidae; (2) new material belonging to Scincomorpha, (3) new material belonging to Anguidae; and (4) the first reported predatory lizard (Platynota) material from the Campanian of New Mexico. The increase in lizard diversity in the “Hunter Wash Local Fauna” expands our understanding of Late Cretaceous squamate taxonomy, distribution, and diversity in the Western Interior of North America (Laramidia). Collectively, the described specimens represent family-level diversity similar to that seen in other Campanian foreland basin deposits of the Western Interior, such as the mid-paleolatitude Kaiparowits Formation of Southern Utah, the higher paleolatitude Dinosaur Park Formation of Southern Alberta, and the lower paleolatitude Aguja Formation of West Texas. The lizards of the “Hunter Wash Local Fauna” represent crucial mid-paleolatitude data from coastal plain depositional settings in Laramidia – 33 allowing for comparisons to more well-studied assemblages at different latitudes and in different depositional settings. 3.1. Introduction The Campanian Fruitland and Kirtland formations (~76-73.5 Ma) (Fassett & Heizler, 2017) of northwestern New Mexico have a rich history of fossil macrovertebrate collection (Osborn & Sternberg, 1923; Ostrom, 1963; Carr & Williamson, 2010), but much less attention has been paid to the microvertebrate assemblage from these formations. In particular, squamate (lizards and snakes) descriptions have been limited to preliminary taxonomic studies (Armstrong-Ziegler, 1978; Armstrong-Ziegler, 1980; Sullivan, 1981). To date, the only formally described squamate taxa from the Fruitland and Kirtland formations are the teiids Chamops segnis and Leptochamops denticulatus (Armstrong-Ziegler, 1978; Armstrong-Ziegler, 1980; Sullivan, 1981), the anguid c.f. Gerrhonotus sp. (Armstrong-Ziegler, 1980), and the ophidian Coniophis cosgriffi (Armstrong- Ziegler, 1978). All four of these taxonomic assignments, while important in establishing the presence of squamates in the Fruitland and Kirtland Formations, have been met with skepticism (Table 1; Estes 1983; Gao & Fox 1996; Nydam & Voci 2007; Longrich, Bhullar & Gauthier, 2012a; Nydam 2013b). Previous authors (Gao & Fox, 1996, Nydam & Voci, 2007) concluded that the referred material to Leptochamops by Armstrong-Ziegler (1978, 1980) can more confidently be referred to amphibian taxa. Indeed, the specimen figured in Armstrong-Ziegler (1980) is at least superficially most similar to amphibians belonging to the family Albanerpetontidae, which possess strongly pleurodont and non-pedicellate teeth bearing labiolingually compressed, usually tricuspid, chisel- like crowns (Sweetman & Gardner, 2012). I agree with previous authors (Gao & Fox, 1996, Nydam & Voci, 2007) that the material described and referenced in Armstrong-Ziegler (1978, 34 1980) (UALP 75137D, E, K, M, N) should at least be referred to Lissamphibia. Specimens belonging to Albanerpetontidae are common in recent collections of microvertebrate material from the Fruitland and Kirtland Formations, and given the similarities between Albanerpetontid tooth- bearing elements and the described Leptochamops specimens in Armstrong-Ziegler (1978, 1980), I suggest that UALP 75137D, E, K, M, and N should be referred to Albanerpetontidae. Unfortunately, the material referred to Leptochamops in Armstrong-Ziegler (1978, 1980) cannot be located, and may have been lost in collections moves and loans between the University of Arizona Laboratory of Paleontology, Wayne State University, and the New Mexico Museum of Natural History & Science in the 1980s (E. Lindsay, N. Volden, pers. comm. to C.H.W., 2019). Additionally, given the host of problematic referrals of Late Cretaceous squamate material to the species Chamops segnis (see Gao & Fox 1996, Nydam 2013a, 2013b for extensive discussion), the referral of fragmentary material in Armstrong-Ziegler (1980) and Sullivan (1981) to Chamops segnis should also be regarded as extremely tentative. The specimen MNA Pl. 1613 is too fragmentary for a confident referral to Chamops given the more recently updated definitions of the genus by Gao & Fox (1996), Nydam & Voci (2007), and Nydam (2013b), who collectively conclude that a referral to “Teiidae, gen. et. sp. indet.” (Gao & Fox, 1996), or “Chamops sp. (Nydam & Voci, 2007), or Chamopsiidae indet.” (Nydam, 2013b), is more appropriate. The referral of UNM FKK-038a to Chamops segnis by Sullivan (1981) was also questioned by Gao & Fox (1996) and Nydam (2013b), with both studies concluding that, though referral of UNM FKK- 038a to Teiidae is appropriate, referral to Chamops segnis is not justified. UNM FKK-038a may have been lost in the transfer of University of New Mexico specimens over to the New Mexico Museum of Natural History (N. Volden pers. comm. To C.H.W., 2019), and could not be re- evaluated in the current study. 35 As discussed by Nydam (2013b), Gao & Fox (1996) found the referral of fragmentary anguid material from the Fruitland/Kirtland formations to Odaxosaurus to be more appropriate than the previous referral to c.f. Gerrhonotus sp. by Armstrong-Ziegler (1980) and Estes (1983). Unfortunately, the material referred to c.f. Gerrhonotus sp. in Armstrong-Ziegler (1980) seems to have also been lost in collections moves and loans between the University of Arizona Laboratory of Paleontology, Wayne State University, and the New Mexico Museum of Natural History & Science in the 1980s (E. Lindsay, N. Volden, pers. comm. to C.H.W., 2019). Additionally, the referral of fragmentary snake vertebrae to the ophidian genus Coniophis (Armstrong-Ziegler, 1978) has been questioned in a recent review of the genus (Longrich, Bhullar & Gauthier, 2012a, Supp. 1). Although referral of MNA Pl. 1612 to Coniophis may not be appropriate, the specimen most certainly belongs to a snake, due to the presence of zygosphene/zygantrum and haemal keel on the ventral surface of the centrum (Romer, 1956). I therefore suggest that MNA Pl. 1612 be referred to as Serpentes indet. until more complete material is recovered. In my review of historical data for the squamate fauna of the Fruitland and Kirtland formations, I encountered two major problems that have been previously summarized (Gao & Fox, 1996, Nydam, 2013b): 1) fragmentary data/incomplete specimens; and 2) outdated and/or inaccurate taxonomic referrals in previous research, which have both led to a lack of clarity in the true taxonomic composition of squamates in the geologic units. The study herein seeks to address these problems by describing newly collected squamate specimens from the Fruitland and Kirtland formations within the context of the previous work summarized above, and an apomorphy-based approach to specimen identification and construction of faunal lists (Bell et al. 2004; Bever, 2005; Nesbitt and Stocker, 2008). This study includes descriptions of specimens referable to Chamopsiidae, Scincomorpha, Anguidae, and Platynota from the “Hunter Wash” faunal zone in 36 the Upper Fruitland and Lower Kirtland formations. The described specimens expand the taxonomic and morphological diversity of lizards within the “Hunter Wash” faunal zone and represent significant new data points in understanding the regional distribution of lizard groups during the Campanian in Western North America. Discussions of biogeographic patterns in Late Cretaceous North American lizards (Nydam, 2013b; Nydam, Rowe, & Cifelli, 2013) have cautiously incorporated the previous erroneous identifications of squamates from the Fruitland & Kirtland formations (Armstrong-Ziegler, 1978, 1980; Sullivan, 1981). At a family taxonomic level, the updated lizard assemblage of the Fruitland and Kirtland formations – representing an important mid-latitude coastal plain depositional setting (Gates et al., 2010) – allow for comparison to well-sampled lizard assemblages from 1) coastal plain depositional settings at higher paleolatitudes (Dinosaur Park Formation – Gao & Fox, 1996), and lower paleolatitudes (Aguja Formation – Nydam, Rowe & Cifelli, 2013; Cerro del Pueblo Formation – Aguillon-Martinez, 2010), and 2) alluvial plain depositional settings at mid- paleolatitudes (Kaiparowits Formation – Nydam, 2013a) and at higher paleolatitudes (Wapiti Formation – Nydam, Caldwell & Fanti, 2010; Nydam, 2013b), (Table 2). The specimens described in detail herein ensure that accurate data from the squamate assemblage of the Fruitland and Kirtland formations can be used for reconstructions of local and regional biogeographic patterns in the future. 3.2. Geologic Setting DMNH loc. 6685, “Black Bowl,” is located in a gray fine-grained sandstone with carbon staining within the upper Fruitland Formation (Fig. 1). DMNH loc. 5204, “Tom’s Dirty Hole,” (Fig. 1) is located in a gray fine-grained sandstone within the lower Kirtland Formation. Though exact stratigraphic location is difficult to discern based on variable interpretations of the 37 interformational contact, both localities lie well within the “Hunter Wash” faunal zone, defined as the fossiliferous horizons in the upper 12.2 meters of the Fruitland Formation and the lower 16.8 m of the Kirtland Formation in the Hunter Wash area (Clemens, 1973; Sullivan & Lucas, 2003; Sullivan & Lucas, 2006). Joyce et al. (2018) called attention to the fact that the definition of the “Hunter Wash” faunal zone is dependent on a clear interformational contact between the Fruitland and Kirtland formations. This is problematic given that considerable disagreement persists over the nature and stratigraphic location of the contact between the Fruitland and Kirtland formations. The Fruitland/Kirtland contact was initially recognized as gradational, though the underlying Fruitland Formation was observed to be typically sandier than the overlying Kirtland Formation (Bauer, 1916). Later work (Fassett & Hinds, 1971; Fassett, 2000; Fassett, 2010) defined the contact as the top of the highest coal or carbonaceous shale in the Fruitland Formation. Given the gradational transition between the Upper Fruitland Formation and the lower shale member of the Kirtland Formation (‘Hunter Wash Member’ of Hunt & Lucas 1992), the top of the highest coal/carbonaceous shale is often obscured in outcrop. Other attempts to define the Fruitland/Kirtland contact (Hunt & Lucas, 1992; Lucas, Hunt & Sullivan, 2006) have placed the top of the Fruitland at the base of the ‘Bisti Member’ or ‘Bisti Bed,’ an indurated but laterally discontinuous sandstone horizon. More work is necessary before a robust lithostratigraphic definition of the Fruitland/Kirtland contact is accepted. Regardless of definition, both localities discussed herein, “Black Bowl” and “Tom’s Dirty Hole,” are well within the recognized horizons of the Hunter Wash Local Fauna. 3.3. Materials & Methods All materials herein were collected by Denver Museum of Nature & Science field crews during the 2014 and 2016 field seasons under United States Federal Bureau of Land Management permit 38 NM14-04S. Specimens were bulk collected in matrix using standard shovels and pick-axes, placed into 15-gallon plastic bags and transported to the Denver Museum of Nature & Science for wet screen-washing and sorting via the methods outlined in Cifelli, Madsen, & Larson (1996), and identification. Specimens were measured and photographed at the Natural History Museum of Los Angeles County using a Keyence VHX-5000 digital microscope. Scanning electron micrographs of the specimens were produced using a Hitachi S-3000 N scanning electron microscope at the Natural History Museum of Los Angeles County. All specimens described in this study are housed in the Earth Sciences Vertebrate Paleontology collections at the Denver Museum of Nature & Science. 3.3.1 Anatomical terminology: I follow the recommendations of Richter (1994), Evans & Searle (2002), and Smith & Dodson (2003), regarding dental anatomical terminology. 3.3.2. Institutional Abbreviations: DMNH: Denver Museum of Nature & Science, Denver, CO, USA; MNA: Museum of Northern Arizona, Flagstaff, AZ, USA; UNM-FKK: Department of Geology, University of New Mexico, Albuquerque, NM, USA; NMHLA/LACM: Natural History Museum of Los Angeles County, Los Angeles, CA, USA; OMNH: Sam Noble Oklahoma Museum of Natural History, Norman, Oklahoma, USA; UALP: University of Arizona Laboratory of Paleontology, Tucson, AZ, USA; UMNH: Natural History Museum of Utah, Salt Lake City, Utah, USA. 3.4. Results 3.4.1. Systematic Paleontology: Chamopsiidae indet. Reptilia Linnaeus, 1758 Squamata Oppel, 1811 Scincomorpha Camp, 1923 39 Boreoteiioidea Nydam, Eaton, & Sankey, 2007 Chamopsiidae Denton & O’Neill, 1995 3.4.1.a. Referred Specimen: DMNH EPV.119583 (jaw fragment). 3.4.1.b. Locality and Horizon: DMNH loc. 6685 “Black Bowl,” Upper Fruitland Formation (Campanian), San Juan County, New Mexico. Within the Ah-She-Sle-Pah Wilderness Study Area. 3.4.1.c. Description: DMNH EPV.119583 (Fig. 2A-F) is a jaw fragment with three partial teeth preserved. The bone to which the teeth attach is too incomplete to assess whether this specimen belongs to the maxilla or the dentary, but the preserved teeth are informative enough to merit description. Tooth attachment is subpleurodont, with the lateral parapet extending less than one third the length of the tooth shaft. Teeth are subcircular in cross-section, and are widely spaced along the tooth row. The bases of the teeth are labiolingually expanded at their mid-shaft, and taper in width occlusally, giving the tooth a barrel-like shape (Fig. 2C-D). One tooth (Fig. 2D) is almost completely preserved, with the tooth crown partially chipped off. This tooth is straight throughout its long axis and not recurved. The crown preserves the base of a central cusp and a mesial/distal cusp (orientation cannot be determined) that are connected by a prominent carina (Fig. 2E-F). 3.4.1.d. Discussion: The tooth attachment of DMNH EPV.119583 (subpleurodont), the tooth shaft shape (barrel-like), and the cross-sectional shape of the teeth (subcircular) are similar to that of Late Cretaceous chamopsiids in North America, particularly specimens associated with the genera Chamops (Maastrichtian Lance Formation, Wyoming, Marsh, 1892; Gilmore, 1928; Estes, 1964; Late Campanian Dinosaur Park Formation, Maastrichtian Frenchman Formation, Alberta, Gao & Fox, 1996; Kaiparowits Formation, Nydam & Voci, 2007, Turonian Smoky Hollow Member of the Straight Cliffs Formation, Utah, Nydam, 2013a), Leptochamops (Maastrichtian Lance Formation, Wyoming, Gilmore, 1928; Estes, 1964; Late Campanian Dinosaur Park Formation, 40 Maastrichtian Frenchman Formation, Alberta Gao & Fox, 1996; Kaiparowits Formation, Utah, Nydam & Voci, 2007), Socognathus (Late Campanian Dinosaur Park Formation, Alberta, Gao & Fox, 1996; Maastrichtian Lance Formation, Wyoming, Longrich, Bhullar & Gauthier, 2012b), and an unnamed chamopsiid from the Maastrichtian Laramie Formation, Colorado (Longrich, Bhullar & Gauthier, 2012b). Subpleurodont teeth have been interpreted as a synapomorphy of Borioteiioidea (Nydam, Eaton, & Sankey, 2007). Both barrel-shaped tooth cross sections and widely spaced tooth positions were considered diagnositic features of Chamopsiidae by Nydam, Caldwell, & Fanti (2010), supporting the referral of DMNH EPV.119583 to this family. Furthermore, the accessory cusp on the most complete tooth of DMNH EPV.119583, connected to the main cusp by a prominent carina, is also a diagnostic feature of Chamopsiidae (Nydam, Caldwell, & Fanti, 2010). The most complete tooth in DMNH EPV.119583 is straight throughout its long axis, which distinguishes it from Socognathus and Meniscognathus, though some variation in this condition may be present in these taxa (Nydam, Caldwell, Fanti, 2010). The development of the prominent mesial/distal carina into an accessory cusp distinguishes DMNH EPV.119583 from other chamopsiid taxa such as Pelsochamops (Makádi, 2013) and Socognathus (Gao & Fox, 1991; Gao & Fox, 1996), in which the carina is not developed such that it forms a cusp. The fragmentary preservation of DMNH EPV.119583 limits my ability to make further taxonomic distinctions, but based on apomorphic features alone, the specimen at least belongs to a chamopsiid that has prominent mesial and distal carina that develop into accessory cusps. 3.4.2. Systematic Paleontology Scincomorpha Camp, 1923 Gen. et sp. indet. 41 3.4.2.a. Referred Specimen: DMNH EPV.119554 (partial left dentary). 3.4.2.b. Locality and Horizon: DMNH 5204, “Tom’s Dirty Hole”, Lower Kirtland Formation (Campanian), San Juan County, New Mexico. Within the Ah-She-Sle-Pah Wilderness Study Area. 3.4.2.c. Description: DMNH EPV.119554 (Fig. 3A-G) is a partial left dentary with three tooth positions, two partial teeth and one complete tooth preserved. The medial and lateral walls of the Meckelian canal are not preserved, but the portion ventral to the subdental shelf remains and has two distinct parallel anteroposteriorly-directed ridges (Fig. 3G). The inferior alveolar canal has one branching canal that terminates laterally with a mental foramen (Fig. 3D). The subdental shelf is prominent and extends medially by twice the tooth shaft cross-sectional diameter. The medial margin of the subdental shelf thickens such that the dorsal surface of the subdental shelf curves dorsally (Fig. 3F). Tooth attachment is pleurodont, with the tooth attached to the lateral parapet for roughly two-thirds of its length (Fig. 3A). A nutrient foramen is present at the base of the posterior-most tooth position. Tooth shafts are slender and cylindrical. Tooth crowns are curved lingually. The tooth crowns are incipiently bicuspid, with the larger, primary cusp forming a medial apex and the smaller, accessory cusp developed on the mesial carina (Fig. 3B). The posterior cusp has a distinct cuspis labialis and a distinct cuspis lingualis, with a weakly-defined carina intercuspidalis connecting them (Fig. 3C). The cuspis labialis, which forms the apex of the cristae mesialis and distalis, is distinctly higher than the cuspis lingualis (the apex of the cristae lingualis anterior and posterior) (Fig. 3C). A weakly-defined posterior portion of the antrum intercristatus is visible on the posterior tooth crown (Fig. 3C). The culmen lateris anterior separates most of the anterior portion of the anterior cusp and wraps medially around the tooth shaft at a shallow angle. Vertical apical striae are present, with a larger vertical groove at the convergent 42 margin between the two cusps. The lingual striae of the tooth crown terminate at the same height as the lateral parapet. Weak apical striae are present on the labial surface of the tooth crown. 3.4.2.d. Discussion: I interpret the structures converging at the cuspis lingualis in DMNH EPV.119554 as cristae lingualis (seen in scincids/lacertids, Kosma 2004), rather than striae dominans (seen in paramacellodids, Kosma 2004), because of several tooth crown features that are observed in scincids and lacertids and not paramacellodids, which are outlined below. 1) bicuspid teeth with a main cusp and a smaller mesial cusp set off from the main cusp can be observed in modern lacertine genera Acanthodactylus, Algyroides, Archaeolacerta, and Darevskia (Kosma 2004). 2) Alggyroides, Archaeolacerta, and Darevskia also possess lingual apical striae similar to those seen in DMNH EPV.119554 (Kosma, 2004). 3) DMNH EPV.119554 also demonstrates tooth morphology similar to that of the fossil scincids Orthrioscincus mixtus from the Upper Campanian Dinosaur Park Formation (Gao & Fox, 1996), southeastern Alberta, Canada, and Estescincosaurus cooki (Estes, 1964; Sullivan, 1997) from the Maastrichtian Lance Creek Formation, Wyoming, USA, in possessing bicuspid teeth with a main cusp and a smaller mesial cusp set off from the main cusp, and a main cusp with lingual striae and weak labial striae. Paramacellodids, such as Paramacellodus and Becklesius hoffstetteri (Kosma 2004), often possess chisel-shaped, unicuspid tooth crowns that are not similar to the morphology seen in DMNH EPV.119554. The cylindrical generalized scincomorphan tooth plan, and similarities with lacertid and scincid tooth crown morphologies, allow us to confidently place DMNH EPV.119554 within Scincomorpha. The temporal distribution of lacertids (only one tentative occurrence from the Mesozoic, Gasca et al. 2007) and the presence of scincids and lizards with scincid-grade tooth crown morphology in numerous geologic units in the Cretaceous of North America (Gao & Fox 1996; Nydam, Rowe & Ciffelli, 2013) suggest that DMNH EPV.119554 most likely belongs to a 43 scincid. However, based solely on the morphological features of the specimen, I limit assignment of DMNH EPV.119554 to Scincomorpha until more complete material is recovered. 3.4.3. Scincomorpha family indeterminate 3.4.3.a. Referred Specimen: DMNH EPV.119567 (osteoderm) 3.4.3.b. Locality and Horizon: DMNH loc. 5204, “Tom’s Dirty Hole”, Lower Kirtland Formation (Campanian), San Juan County, New Mexico. Within the Ah-She-Sle-Pah Wilderness Study Area. 3.4.3.c. Description: DMNH EPV.119567 (Fig. 4) is a rectangular osteoderm with a weak keel running longitudinally up the center of the external surface. The external surface of the osteoderm is generally smooth with small pits concentrated near the central keel (Fig. 4B). The external pits do not penetrate through to the internal surface of the osteoderm. The internal surface of the osteoderm is smooth and concave toward the external surface. The anterior imbrication facet is broken off, with only a small, triangular portion preserved (Fig. 4B). 3.4.3.d. Discussion: The presence of a central keel on the external surface of the osteoderm, the limited surficial sculpturing, and the large size of the osteoderm indicate that DMNH EPV.119567 belongs to a scincomorphan lizard (sensu Broschinski and Sigogneua-Russell, 1996). However, I cannot confidently associate this isolated osteoderm with any of the taxa described herein, nor can I confidently associate its anatomical position on the body. Similar large, rectangular osteoderms with a central external keel and limited surficial sculpturing have been assigned to Scincomorpha in both the paracontemporaneous Kaiparowits Formation Southern Utah (Nydam, 2013a), and the paracontemporaneous Aguja Formation of West Texas (Nydam, Rowe & Cifelli, 2013). Because these lizard assemblages bracket the Fruitland/Kirtland Formations to the Northwest (Kaiparowits 44 Formation) and Southeast (Aguja Formation), it is predictable to find scincomorphan-grade osteoderms within the “Hunter Wash Faunal Zone”. 3.4.4. Systematic Paleontology Anguimorpha Fürbringer, 1900 Anguidae Gray, 1825 Odaxosaurus Gilmore, 1928 Species indet. 3.4.4.a. Referred Specimen: DMNH EPV.119555 (posterior left dentary). 3.4.4.b. Locality and Horizon: DMNH loc. 5204, “Tom’s Dirty Hole”, Lower Kirtland Formation (Campanian), San Juan County, New Mexico. Within the Ah-She-Sle-Pah Wilderness Study Area. 3.4.4.c. Description: DMNH EPV.119555 (Fig. 5A-G) is the posterior portion of a left dentary, indicated by the presence of a posteromedial “notch” in the subdental lamina (Fig. 5G). Six tooth positions are preserved (Fig. 5A), with the anterior-most tooth partially preserved (#1, Fig. 5A), and the five posterior-most teeth completely preserved (#2 -6, Fig. 5A). Tooth attachment is pleurodont, with tooth bases labiolingually expanded and attached at an oblique angle to the subdental shelf (Fig. 5F). A faintly preserved nutrient foramina can be seen at the base of the second posteriormost tooth (Fig. 5F, G). Tooth shaft height and tooth base expansion lessens sharply from anterior to posterior. Tooth shafts are thick and stocky in overall shape, indicative of a more posterior position in the dentary. The four anteriormost teeth showcase triangular basal excavations posterolingually to the tooth bases (Fig. 5F, G), while the fifth anterior-most tooth showcases a circular resorption pit (Fig. 5F). This pattern is indicative of a progressive anterior- to-posterior tooth replacement strategy. Tooth crowns are incompletely preserved and do not 45 preserve enamel on the lingual surface, but are gently recurved and chisel-shaped (Fig 5B, F). The enamel on the third anteriormost tooth crown is preserved on the labial surface, and possesses weak labial apical striae (Fig. 5C, E). The cutting edge of the tooth crowns form a medially-pointed V-shape (Fig. 5G). 3.4.4.d. Discussion: DMNH EPV.119555 is referable to Anguimorpha based on synapomorphic features concerning the development of replacement teeth: 1) replacement teeth develop posterolingually to tooth midline (Estes, de Quieroz, & Gauthier, 1988); 2) small resorption pits present (Estes, de Quieroz, & Gauthier, 1988). Furthermore, DMNH EPV.119555 is referable to Anguidae on the basis of tooth crown morphology: 1) in occlusal view, cutting edge of posterior teeth forming an inwardly-pointing V (Fig. 5G); 2) crown apex lies slightly posterior and lingual to center of long axis of tooth (Fig. 5F, G); 3) crown is commonly rotated about the long axis of the tooth and apex tipped posteriorly, so that in profile the leading edge is prominently convex and extends back to the apex, giving a recurved, chisel-shape to the crown (Fig. 5F) (Estes, 1964). Additionally, striations on the labial surface of the tooth crown of DMNH EPV.119555 are noteworthy (Fig. 5C, E), since striations on both labial and lingual surfaces on the tooth crowns have historically been considered a diagnostic character of Anguidae (Gauthier, 1982; but recent evidence (Nydam, 2013a) suggests that lingual striations on tooth crowns may not be a requisite diagnostic character in anguid taxa such as Odaxosaurus roosevelti). The lack of preservation of lingual surfaces of the teeth of DMNH EPV.119555 means I cannot assess this character fully. However, because striae are present at least on the labial surface of the tooth crown of DMNH EPV.119555, this specimen can be used to make further taxonomic distinctions pending the recovery of more complete material. 46 The only known anguid taxa from the Late Campanian of North America belong to the genus Odaxosaurus: O. piger from the Aguja Formation (Nydam, Rowe & Cifelli, 2013), O. priscus and O. roosevelti from the Kaiparowits Formation (Nydam, 2013a), O. priscus from the Dinosaur Park Formation (Gao & Fox, 1996), and O. new species from the Cerro del Pueblo Formation (Aguillon-Martinez, 2010). The close spacing of the teeth in DMNH EPV.119555 is similar to the close spacing of teeth in O. roosevelti (Nydam, 2013a) and O. piger (Nydam, Rowe & Cifelli, 2013), while the teeth in O. priscus (Nydam, 2013a) and O. new species (Aguillon- Martinez, 2010) are generally spaced further apart from one another. Additionally, the tooth crowns in DMNH EPV.119555 exhibit less “mesiodistal flaring” than that observed in O. piger (Nydam, 2013a; Nydam, Rowe & Cifelli, 2013) and O. new species (Aguillon-Martinez, 2010), but this could likely to be an artifact of poor preservation and/or tooth wear in DMNH EPV.119555. The preserved anatomical features highlighted above in DMNH EPV.199555, in addition to the presence of three species of Odaxosaurus in geographically bracketing paracontemporaneous lizard faunas (Kaiparowits Formation, Southern Utah; Aguja Formation, West Texas), merit a tentative referral to Odaxosaurus sp. pending the recovery of more complete material. Because the only other described specimens from the Fruitland/Kirtland formations (UALP 75137-F: left dentary fragment; UALP 75317-G: left dentary fragment; Armstrong- Ziegler, 1980) referable to Odaxosaurus cannot be located in museum collections, DMNH EPV.119555 is a critical representative specimen for the genus in the Late Campanian of New Mexico. 3.4.5. Anguidae indet. “Hunter Wash” Anguidae Osteoderm Morphotype A 47 3.4.5.a. Referred specimens: DMNH EPV.119455 (trunk osteoderm), DMNH EPV.199457 (cranial osteoderm). 3.4.5.b. Locality/Horizon: DMNH loc. 6685 “Black Bowl,” Upper Fruitland Formation (Campanian), San Juan County, New Mexico (DMNH EPV.119455). DMNH loc. 5204, “Tom’s Dirty Hole”, Lower Kirtland Formation (Campanian), San Juan County, New Mexico (DMNH EPV.119577). Both localities within the Ah-She-Sle-Pah Wilderness Study Area. 3.4.5.c. Description: DMNH EPV.119455 (Fig. 6A, B) is a flat (i.e. no externally-directed curvature or keel) rectangular trunk osteoderm with a large, distinctive anterior imbrication facet and narrow lateral imbrication facets. The external surface is ornamented with a series of subcircular pits that are oriented such that their openings radiate laterally and away from the center of the osteoderm (Fig. 6A). The right lateral and posterior edge of the osteoderm is broken. DMNH EPV.119457 (Fig. 6C-E) is a flat, hexagonal, cranial osteoderm with narrow imbrication facets on the anterior three sides of the specimen (Fig. 6C). The central imbrication facet is concave inward toward the center of the osteoderm (Fig. 6C-D). This indicates that the osteoderm was located at the margin of a foramen in the skull, though because this specimen is isolated, it is difficult to determine its exact location. On the internal surface (Fig. 6E), two well-defined articular facets are angled toward the outer margin of the osteoderm for articulation with at least two additional osteoderms on the skull. The external surface of the osteoderm is heavily ornamented with a series of subcircular pits that are connected by vascular canals that radiate from the center of the osteoderm. 3.4.5.d. Discussion: See below. 3.4.6. “Hunter Wash” Anguidae Osteoderm Morphotype B 3.4.6.a. Referred Specimens: DMNH EPV.119577 (osteoderm). 48 3.4.6.b. Locality/Horizon: DMNH loc. 5204, “Tom’s Dirty Hole”, Lower Kirtland Formation (Campanian), San Juan County, New Mexico. Within the Ah-She-Sle-Pah Wilderness Study Area. 3.4.6.c. Description: DMNH EPV.119577 (Fig. 6F, G) is a flat, ovoid trunk osteoderm with a small, weakly-defined imbrication facet and a narrow right-lateral imbrication facet on the external surface (Fig. 6F). These two imbrication facets are connected to one another in such a way that they form a single continuous surface on the anterior and right lateral margins. The external surface of DMNH EPV.119577 is heavily ornamented with irregularly branching grooves and ridges, with subcircular pits interspersed between the ridges. 3.4.6.d. Discussion: Similar subrectangular/ovoid trunk osteoderms and polygonal cranial osteoderms, both with external surficial sculpting, are commonly associated with modern anguid genera, including Ophisaurus, Elgaria, Gerrhonotus, Mesapsis, Abronia, and Barisia (Mead et al. 1999). Additionally, similar osteoderms attributed to Anguidae have commonly been recovered from Upper Cretaceous microvertebrate localities in Montana (Judith River Formation, Sahni, 1972), Wyoming (Lance Formation, Estes, 1964), Canada (Dinosaur Park Formationm, Gao & Fox, 1996), Utah (Kaiparowits Formation, Nydam, 2013a), Texas (Aguja Formation, Nydam, Rowe & Ciffelli, 2013), and Mexico (Cerro del Pueblo Formation, Aguillon-Martinez, 2010). I conditionally assign the osteoderms described herein to Anguidae due to the shape (subrectangular/ovoid for trunk osteoderms, polygonal for cranial osteoderms), and external surficial sculpting patterns (subcircular pits and narrow, irregular grooves) (Mead et al. 1999). Subtle differences in an osteoderm’s external surface sculpting is commonly used for taxonomic distinction in fossil and modern anguid lizards (Meszoely & Ford 1976, Mead et al. 1999, Mead et al. 2012).I will refrain from discussing lower-level taxonomic affinities until more complete specimens are recovered from the Fruitland/Kirtland formations; however, I do recognize that 49 there at least two distinct morphotypes of osteoderm within these described specimens. “Hunter Wash” Anguidae Osteoderm Morphotype A consists of DMNH EPV.119455 and DMNH EPV.119457 (Fig. 6A-E). The external surfaces of both osteoderms are covered in small, 50-100 µm-diameter pits that are surficial expressions of a network of vessels that radiate from roughly the center of the osteoderm. “Hunter Wash” Anguidae Osteoderm Morphotype B consists solely of DMNH EPV.119577 (Fig. 6F-G). The external surface of “Hunter Wash” Anguidae Osteoderm Morphotype B differs from Morphotype A because it is ornamented with irregularly branching grooves and ridges, with additional subcircular pits interspersed in between the ridges. 3.4.7. Systematic Paleontology Platynota Duméril and Bibron, 1836 Platynota indet. 3.4.7.a. Referred Specimen: DMNH EPV.119569 (jaw fragment) 3.4.7.b. Locality and Horizon: DMNH 5204, “Tom’s Dirty Hole”, Lower Kirtland Formation (Campanian), San Juan County, New Mexico. Within the Ah-She-Sle-Pah Wilderness Study Area. 3.4.7.c. Description: DMNH EPV.119569 (Fig. 7 A-F) is a jaw fragment with two tooth positions and one partial tooth preserved. The lateral surface of the jaw is smooth with no evidence of fused osteoderms. The lateral surface swells where the preserved tooth articulates with the lateral wall of the specimen. A cluster of five posteriorly-directed mental foramina are arranged on the surface of the jaw near the articulation of the preserved tooth and the lateral parapet (Fig. 7 D). On the ventrolateral/dorsolateral surface of the specimen, a v-shaped groove is directed posteriorly along the surface (Fig. 7 D-F, see Discussion below), and terminates with an anteriorly-excavated, rounded fossa. Two tooth positions are preserved, while one tooth base with the basal portion of 50 the crown is preserved. Tooth attachment is subpleurodont, with the lateral attachment extending one-third of the tooth height. The base of the tooth is subcircular and possesses basal infoldings that contact the circumferential ridge of cementum surrounding the base of the tooth at a sharp angle. The lingual basal infoldings terminate below the lateral parapet. A large, medially directed nutrient foramen is present at the base of the tooth (Fig. 7 C). The tooth crown is broken off, but the basal portion of the crown exhibits wearing of enamel. The mesial carina (distal carina not preserved) is positioned labially. 3.4.7.d. Discussion: DMNH EPV.119569 is referable to Platynota on the basis of tooth morphology: 1) the expanded base of the tooth has been used as a diagnostic character for Platynota (Gao & Fox, 1996) and less inclusive groups within Platynota (Platynota exclusive Dorsetisaurus pubeckensis, Conrad, 2008); 2) the basal enamel infoldings have also been used to diagnose less inclusive groups within Platynota (e.g. Varanoidea, Estes, de Quieroz, & Gauthier, 1988; Parasaniwa wyomingensis + Parviderma inexacta + Varanoidea, Conrad, 2008). I compared DMNH EPV.119569 to maxillae and dentaries belonging to modern platynotan specimens (Heloderma suspectum (LACM 165160; LACM 163853; LACM 163855), H. horridum (LACM 163852; LACM 163854; LACM 159136), Varanus bengalensis (LACM 159019; LACM 163952- 54; LACM 159042), V. salvator (LACM 163949)), and could not find a structure similar to the posteriorly-projecting v-shaped groove. Additionally, figured specimens belonging to paracontemporaneous fossil platynotans from North America, including Parasaniwa cynochoros from the Kaiparowits Formation, southern Utah (UMNH VP 21180, partial right maxilla, Nydam, 2013a), c.f. Parasaniwa wyomingensis from the Aguja Formation, West Texas (OMNH 30882, partial ?right dentary, Nydam, Rowe & Cifelli, 2013), Paraderma bogerti (AMNH FARB 8504, partial right maxilla, Sahni, 1972), and Parasaniwa c.f. Parasaniwa wyomingensis from the Cerro 51 del Pueblo Formation, Coahuila, Mexico (SEPCP 9/582, dentary, Aguillon-Martinez, 2010) do not showcase a v-shaped groove in a similar position. If DMNH EPV.119569 is a maxilla, the groove could be interpreted as an articulation facet with the jugal, but no structure exists in such an extreme lateral position in the posterior maxillae of the surveyed modern platynotan specimens. If DMNH EPV.119569 is a dentary, then the v-shaped groove could be interpreted as the anterior termination of the Meckelian canal, but DMNH EPV.119569 is not as curved as the symphyseal regions of the observed modern platynotan specimens, and the Meckelian canal is primarily exposed medially at the anterior end of the dentary. Alternatively, the v-shaped groove could be an articulation surface with the lateral articulation facet of the coronoid or surangular, but modern platynotans observed in the collection at NHMLA and figured fossil platynotan specimens in primary literature (see above for specimen numbers and references) do not exhibit an articulation surface so ventrally-located beneath the posterior end of the dentary. The foramen and groove could also be neurovascular in nature. The unique position of the groove on DMNH EPV.119569 may be an autapomorphic feature of this particular platynotan, however more complete material is needed to determine the anatomical relationships of this structure. The presence of Platynota in the Fruitland Formation is to be expected, as the group has a wide distribution in Late Campanian deposits in Laramidia, including the Cerro del Pueblo Formation (Aguillon-Martinez, 2010) in Coahuila, Mexico, the Aguja Formation in west Texas, USA (Nydam, Rowe & Ciffelli, 2013), the Kaiparowits Formation in southern Utah, USA (Nydam, 2013a), the Mesaverde Formation in central Wyoming, USA (Demar & Breithaupt, 2006), the Judith River Formation in northern Montana, USA (Sahni, 1972), and the Dinosaur Park Formation in southeastern Alberta, Canada (Gao & Fox, 1996). Given the rich history fossil vertebrate collection in the Fruitland and Kirtland formations, however, it is unexpected and 52 significant that no platynotan material had been collected or described until the study herein. DMNH EPV.119569 offers the first definitive evidence of platynotan lizards in the Late Campanian of New Mexico, and fills in a critical gap in the regional distribution of Platynota in Laramidia. 3.5. Discussion 3.5.1 Squamate diversity and biogeography on Laramidia The fossils described above represent important additions to the record of Late Cretaceous lizards in the San Juan Basin. The non-chamopsiid scincomorphan specimen (DMNH EPV.119554, Fig. 3) and the platynotan specimen (DMNH EPV.119569, Fig. 7) represent the first described occurrences of their respective groups within the Fruitland and Kirtland formations, while the chamopsiid specimen (DMNH EPV.119583, Fig. 2) and the anguid specimens (DMNH EPV.119555, Fig. 5; DMNH EPV.119455, Fig. 6A-B; DMNH EPV.199457, Fig. 6C-E; DMNH EPV.119577. Fig. 6F-G) represent additions to previous descriptions based on fragmentary data (Armstrong-Ziegler, 1978, 1980; Sullivan, 1981). This has intriguing implications not only for the diversity of lizards within the Fruitland and Kirtland formations, but also for regional and continental biogeographic patterns and lizard family-level dispersal in Campanian North America. As discussed extensively in previous work (Nydam, 2013b; Nydam, Rowe & Ciffelli, 2013), chamopsiids are commonly found throughout mid-latitude and higher-latitude localities in Laramidia, while no specimens have been reported south of the paleolatitude of 40° N (Fig. 8A). This pattern suggests that Chamopsiidae was restricted to mid-to-northern Laramidian ecosystems and might have only tolerated subtropical climates (Nydam, Rowe & Ciffelli, 2013). Although tentative chamopsiid material (discounting Leptochamops material since identified as amphibian) has been described from the Fruitland Formation (Armstrong-Ziegler, 1980; Sullivan, 1981, 53 present study), the overall record for the unit remains extremely fragmentary. What makes chamopsiids from the Fruitland and Kirtland formations especially important is that they occupy the southernmost known distribution for the family during the Late Campanian. The Fruitland and Kirtland Formations could therefore be critical for future work assessing chamopsiid distributional patterns at geographic “faunal zone” boundaries (Gates et al., 2010). This synergistic biogeographic work necessitates apomorphy-based revision of extremely common Late Campanian chamopsiid genera such as Chamops and Leptochamops, as well as recovering more complete material in field surveys, in order to describe detailed geographic distribution and diversity patterns in this family (Gao & Fox, 1996; Nydam & Voci, 2007; Nydam, 2013b; Nydam, Rowe & Ciffelli, 2013). Although the lower-level taxonomic affinities of the scincomorphan specimen (DMNH EPV.119554, Fig. 3) cannot be determined from its morphological characteristics alone, it shares enough overlapping features with modern scincids and Late Campanian North American scincids to be included in a tentative biogeographic comparison (Fig. 8B). Scincids are comparatively rare in the Late Campanian of Laramidia, but have been reported from the Dinosaur Park Formation in Alberta (Gao & Fox, 1996) and the Aguja Formation in West Texas (Nydam, Rowe & Cifelli, 2013). The “Hunter Wash” scincid-grade specimen adds an important mid-paleolatitude data point to the distribution of the clade on Laramidia, but occurrences in comparison to other lizard families in Late Campanan Laramidia remains rare (Fig. 8), either due to true lack of abundance, lack of preservation, and/or undersampling. Late Campanian anguids, which are mostly comprised of the genus Odaxosaurus, have been reported from every paracontemporaneous geologic unit from Laramidia except for the Two Medicine Formation in Montana, USA, and the Wapiti Formation in Alberta, Canada (Nydam, 54 Rowe & Ciffelli, 2013). Anguids range from the Cerro del Pueblo Formation in Coahuila, Mexico (Aguillon-Martinez, 2010) to the Dinosaur Park Formation in Alberta, Canada (Gao & Fox, 1996) (Fig. 8C). DMNH EPV.119555, Odaxosaurus sp., from the “Hunter Wash Local Fauna” adds to a growing dataset of occurrences of Odaxosaurus in Southern Laramidia. With three named species (O. piger, Aguja Formation, West Texas, Nydam, Rowe & Cifelli, 2013; O. priscus, O. roosevelti, Kaiparowits Formation, Southern Utah, Nydam, 2013a) and one potential new species (O. new species, Cerro del Pueblo Formation, Coahuila, Mexico, Aguillon-Martinez, 2010), Odaxosaurus represents the only multi-specific lizard genus known from the Late Campanian of North America (Table 2). Though DMNH EPV.119555 is too poorly preserved to merit species-level identification, it would not be surprising if it represented a distinct species of Odaxosaurus, given the presence of at least three different species of Odaxosaurus mentioned above in geographically- bracketing lizard faunas in Southern Laramidia. The platynotan specimen is the first described occurrence of predatory lizards in the Fruitland and Kirtland Formations. Platynotans were widely distributed in the Campanian of North America, with specimens reported from the Cerro del Pueblo Formation in Coahuila, Mexico (Aguillon-Martinez, 2010), to the Dinosaur Park Formation in Alberta (Gao & Fox, 1996) (Fig. 8D). Given this near ubiquitous distribution of Platynota in Laramidia, the recovery of platynotan specimens from the Fruitland/Kirtland formations is predictable. However, the fact that DMNH EPV.119569 is the only recovered Platynota specimen from the Fruitland/Kirtland formations suggests that their abundance in microvertebrate assemblages in the Late Campanian of New Mexico is relatively low, either due to a true low abundance, preservation bias, or collection bias. 55 3.6. Conclusions The new chamopsiid, scincomorphan, anguid, and platynotan material from the “Hunter Wash” faunal zone of the Fruitland and Kirtland formations of northwestern New Mexico represent important primary data points in examining lizard diversity and distribution on both a local temporal scale and on a regional paleogeographic scale. The two lizard-bearing fossil localities in the “Hunter Wash” faunal zone, DMNH loc. 6685, “Black Bowl”, and DMNH loc. 5204, “Tom’s Dirty Hole”, preserve lizard taxa exclusive to one another with a small amount of overlap in Anguidae Osteoderm Morphotype A. This suggests that local depositional environment could be a major source of bias in the preservation of specfic lizard taxa within the Fruitland/Kirtland formations – a phenomenon observed in most other Laramidian fossil squamate localities (Nydam, 2013b). 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A new albanerpetontid amphibian from the Barremian (Early Cretaceous) Wessex Formation of the Isle of Wight, southern England. Acta Palaeontologica Polonica, 58(2), 295-325. Wiersma JP, Irmis RB. 2018. A new southern Laramidian ankylosaurid, Akainacephalus johnsoni gen. et sp. nov., from the upper Campanian Kaiparowits Formation of southern Utah, USA. PeerJ. 6:e5016; DOI 10.7717/peerj.5016. 62 Tables Table 1. Summary of previously described squamate material from the Fruitland and Kirtland formations, including suggested changes in taxonomic referral. Original Taxonomic Assignment (Armstrong-Ziegler, 1978, 1980; Sullivan, 1981) Suggested Taxonomic Change Scincomorpha Borioteiioidea Chamopsiidae Leptochamops denticulatus Lissamphibia (Gao & Fox, 1996; Nydam & Voci, 2007) Albanerpetontidae (Present study) Scincomorpha Borioteiioidea Chamopsiidae Chamops segnis Teiidae gen. et sp. indet. (Gao & Fox, 1996); Chamops sp. (Nydam & Voci, 2007); Chamopsiidae indet. (Nydam, 2013b; present study) Anguimorpha Anguidae c.f. Gerrhonotus sp. Odaxosaurus (Gao & Fox 1996; Nydam 2013b; present study); c.f. Gerrhonotus sp. (Estes 1983) Serpentes Alethenophidia Coniophis cosgriffi “unwarranted” generic referral (Longrich, Bhullar & Gauthier, 2012); Serpentes indet. (present study) 63 Table 2. Lizard faunas of select Late Campanian geologic units in the Western Interior of North America. Geologic units arranged in descending order of geographic location, from North to South. Formation Identified Scincomorpha Identified Anguimorpha Identified Serpentes Wapiti (Nydam, Caldwell & Fanti, 2010) – Central Alberta Scincomorpha Borioteiioidea Chamopsiidae - Socognathus unicuspis Scincomorpha indet. - Kleskunsaurus grandeprairiensis None reported None reported Dinosaur Park (Listed as Oldman Formation in Gao & Fox, 1996) – Southern Alberta Scincomorpha Borioteiioidea Chamopsiidae - Chamops sp. -Leptochamops - Socagnathus Scincidae -Orthrioscincus ?Cordylidae Incertae sedis - Glyptogenys - Sphenosiagon - Gerontoseps Anguimorpha Xenosauridae - ?Exostinus sp. Anguidae - Odaxosaurus priscus Platynota - Parasaniwa n. sp. - c.f. P. wyomingensis Helodermatidae - Labriodectes Varanidae - Palaeosaniwa None reported Kaiparowits (Nydam, Eaton, & Sankey, 2007; Nydam & Voci, 2007; Nydam, 2013a) – Southern Utah Scincomorpha Borioteiioidea Chamopsiidae - Peneteius saueri - Meniscognathus molybrochoros - Chamops sp. c.f. C. segnis - Leptochamops - Tripennaculus eatoni Contogeniidae - Palaeoscincosaurus pharkidodon c.f. Scincoidea Paramacellodid/Cordylid Grade Kaiparowits Morphotype A-G Anguimorpha Anguidae - Odaxosaurus roosevelti - Odaxosaurus priscus Xenosauridae - ?Exostinus Platynota - Parasaniwa cynochoros Kaiparowits Morphotype H-J Serpentes Alethenophidia - Coniophis sp. Fruitland/Kirtland (Updated with current taxonomic IDs) – Northwest New Mexico Scincomorpha Borioteiioidea -Chamopsiidae indet. Scincomorpha indet. - ?Scincidae Anguimorpha Anguidae. - Odaxosaurus sp. - Anguidae indet. Platynota - Platynota indet. Serpentes - Serpentes indet. Aguja (Nydam, Rowe & Ciffelli 2013) – West Texas Scincomorpha cf. Xantusiidae - Catactegenys solaster Scincomorpha indet. - Apsgnathus triptodon - Unnamed scincid-grade taxon - aff. Scincomorpha Anguimorpha Anguidae - Odaxosaurus piger - Anguidae indet. - aff. Xenosauridae Platynota - cf. Parasaniwa wyomingensis Serpentes - Serpentes indet. Cerro del Pueblo (Aguillon-Martinez, 2010) – Coahuila, Mexico Scincomorpha Borioteiioidea Chamopsiidae - Peneteius sp. Anguimorpha Anguidae - Odaxosaurus new sp. Platynota - cf. Parasaniwa wyomingensis Helodermatidae - Paraderma cf. P. bogerti Varanidae - Palaeosaniwa c.f. P. canadensis Serpentes Alethenophidia - Coniophis sp. 64 Figures Figure 1. Surface exposures of the Fruitland and Kirtland formations in the San Juan Basin of northwestern New Mexico (A), with a detailed map of the region surrounding the Ah-Shi-Sle-Pah Wilderness Study Area (B). Approximate locations of the two localities discussed are indicated with stars: 1=DMNH loc. 6685 “Black Bowl,” 2=DMNH loc. 5204 “Tom’s Dirty Hole.” 65 Figure 2. DMNH EPV.119583, Chamopsiidae indet. jaw fragment from the “Hunter Wash Local Fauna”, Fruitland Formation. A. medial view. B. lateral view C. scanning electron micrograph, medial view. D. scanning electron micrograph, medial view, perpendicular to labiolingual axis of complete tooth crown. E. scanning electron micrograph, lateral view. F. Scanning electron micrograph, occlusal view. 66 Figure 3. DMNH EPV.119554, Scincomorpha, partial left dentary, from the “Hunter Wash Local Fauna”, Fruitland Formation. A. medial view; B. medial view, zoom (scanning electron micrograph); C, line drawing of anterior tooth in medial view; D. lateral view; E. lateral view, zoom (scanning electron micrograph); F. occlusal view; G. ventromedial view (scanning electron micrograph). Abbreviations: Inf. Alv. Canal: Inferior Alveolar Canal. 67 Figure 4. DMNH EPV.119567, Scincomorpha indet. osteoderm from the “Hunter Wash Local Fauna”, Kirtland Formation. A. external view. B. Scanning electron micrograph, external view. Abbreviations: Imb. facet: Anterior imbrication facet; Ext. keel: external keel. 68 Figure 5. DMNH EPV.119555, Anguidae posterior left dentary from the “Hunter Wash Local Fauna”, Kirtland Formation. A. medial view. Numbers indicate preserved tooth positions: 1 = anteriormost, 6= posteriormost; B. lateral view; C. lateral view, zoom; D. scanning electron micrograph, lateral view; E. scanning electron micrograph, lateral view, zoom; F. scanning electron micrograph, medial view; G. scanning electron micrograph, occlusal view. Abbreviations: Nut. frm. Nutrient foramen; Res. pit: Resorption pit. 69 Figure 6. Anguidae indet. osteoderms from the “Hunter Wash Local Fauna”, Fruitland/Kirtland formations. A-E: “Hunter Wash” Anguidae Osteoderm Morphotype A. A. DMNH EPV.119455 in external view; B. scanning electron micrograph, external view; C. DMNH EPV.119457 in external view; D. scanning electron micrograph, external view; E. scanning electron micrograph, internal view; F-G: “Hunter Wash” Anguidae Osteoderm Morphotype B. F. DMNH EPV.119577 in external view; G: scanning electron micrograph, external view. Abbreviations: Ant. imb. facet: Anterior imbrication facet; Art. Surf: Articular surface. Imb. facet: Imbrication facet; Lat. Imb. facet: Lateral imbrication facet. 70 Figure 7. DMNH EPV.119569, Platynota indet., jaw fragment from the “Hunter Wash Local Fauna”, Kirtland Formation. A: medial view; B: lateral view; C: scanning electron micrograph, medial view; D: scanning electron micrograph, lateral view; E: scanning electron micrograph, ventral view; F: scanning electron micrograph, posterior view. Abbreviations: Ment. Frm.: Mental Foramina; Nut. frm: Nutrient foramina. 71 Figure 8. Late Campanian latitudinal distribution of lizard groups described in this study, modified from Nydam (2013b), Nydam, Rowe & Ciffelli (2013) and Wiersma & Irmis (2018). Dots indicate squamate-bearing Campanian geologic units, with star representing locality of newly described Fruitland/Kirtland specimens. A: distribution of Chamopsiidae (yellow). B: distribution of Scincidae (red). Question mark at the Fruitland/Kirtland occurrence indicates uncertainty of specimen DMNH EPV.119554 belonging to Scincidae. C: distribution of Anguidae (green). C: distribution of Platynota (blue). Geologic Units: 1. Wapiti Formation (Nydam, Caldwell & Fanti, 2010); 2. Dinosaur Park Formation (Gao & Fox, 1996); 3. Two Medicine Formation Demar et al. (2012); 4. Judith River Formation (Sahni, 1972); 5. Mesa Verde Formation (Demar & Breithaupt, 2006); 6. Kaiparowits Formation (Nydam, 2013a; Nydam, Eaton & Sankey, 2007; Nydam & Voci, 2007; Nydam & Fitzpatrick, 2009); 7. Fruitland/Kirtland Formations (Armstrong-Ziegler, 1978; Armstrong-Ziegler, 1980; Sullivan, 1981; Present Study); 8. Aguja Formation (Nydam, Rowe & 72 Ciffelli, 2013); 9. Cerro del Pueblo Formation (Aguillon-Martinez, 2010). Dotted line indicates approximate boundary between the alluvial plain depositional environment (west of line) and the coastal plain depositional environment (east of line) (Gates et al., 2010). Paleolatitudes from Lehman (1997, and included references). Mean annual paleotemperature estimates from Lehman (1997, and included references), Miller et al. (2013), Estrada-Ruiz et al. (2010), Gates et al. (2010, and included references), and Manchester et al. (2010). 73 CHAPTER 4: A BIASED FOSSIL RECORD CAN PRESERVE RELIABLE PHYLOGENETIC SIGNAL This paper was published as: Woolley, C. H., J. R. Thompson, Y.-H. Wu, D. J. Bottjer, and N. D. Smith. 2022. A biased fossil record can preserve reliable phylogenetic signal. Paleobiology 48(3):480-495. Abstract The fossil record is notoriously imperfect and biased in representation, hindering our ability to place fossil specimens into an evolutionary context. For groups with fossil records mostly consisting of disarticulated parts (e.g., vertebrates, echinoderms, plants), the limited morphological information preserved sparks concerns about whether fossils retain reliable evidence of phylogenetic relationships, and lends uncertainty to analyses of diversification, paleobiogeography, and biostratigraphy in Earth history. To address whether a fragmentary past can be trusted, we need to assess whether incompleteness affects the quality of phylogenetic information contained in fossil data. Herein, I characterize skeletal incompleteness bias in a large dataset (6,585 specimens; 14,417 skeletal elements) of fossil squamates (lizards, snakes, amphisbaenians, and mosasaurs). I show that jaws + palatal bones, vertebrae, and ribs appear more frequently in the fossil record than other parts of the skeleton. This incomplete anatomical representation in the fossil record is biased against regions of the skeleton that contain the majority of morphological phylogenetic characters used to assess squamate evolutionary relationships. Despite this bias, parsimony- and model-based comparative analyses indicate that the most frequently-occurring parts of the skeleton in the fossil record retain similar levels of phylogenetic signal as parts of the skeleton that are rarer. These results demonstrate that the 74 biased squamate fossil record contains reliable phylogenetic information, and support our ability to place incomplete fossils in the Tree of Life. 4.1. Introduction The fossil record is a fundamental natural historical archive for understanding evolution and Earth history. Without information from fossils, we would have considerably less knowledge concerning the extinction and emergence of lineages (Sun et al. 1998; Valentine et al. 1999; Field et al. 2020), the nature of biotic crises (Sun et al. 2012; Lyson et al. 2019; Petsios et al. 2019), and major phenotypic innovations in Earth’s flora and fauna (Daeschler et al. 2006; Murdock and Donoghue 2011; Stein et al. 2012). But behind the illuminating biological information contained in the fossil record is the reality that fossil data are inherently incomplete (Darwin 1859; Foote and Sepkoski 1999; Smith 2001; Kidwell and Holland 2002), due to geological factors (Raup 1976; Smith and McGowan 2005), factors related to fossil preservation (e.g., taphonomic bias, Sansom et al. 2010) and asymmetrical research interest and sampling intensity among workers (e.g., sampling bias, Smith 1994; Smith 2001). These biases have been characterized in the fossil record of a variety of organismal groups (Crane et al. 2004; Brocklehurst et al. 2012; Dean et al. 2016; Driscoll et al. 2019) and a growing number of sampling proxies can be used to account for the multitude of factors that distort paleobiological data. As a result, our ability to explore major questions related to biodiversity in the fossil record is enhanced, but methodological problems remain (Dean et al. 2016; Sakamoto et al. 2017). Furthermore, the patterns of biases associated with a majority of fossil groups are uncharacterized, and the association between biased records and phylogenetic data content remains underexplored (Sansom et al. 2010; Sansom 2015; Sansom et al. 2017; Brocklehurst and Benevento 2020). 75 Taphonomic and sampling biases still represent consistent barriers to reconstructing the phylogenetic relationships of fossil organisms (Patterson 1981; Sansom et al. 2010; Sansom 2015; Sansom et al. 2017, Brocklehurst and Benevento 2020), which are essential to the evolutionary frameworks that synthetic studies of biodiversity (Raup 1979), biostratigraphy (Norell and Novacek 1992), and paleobiogeography (Benson et al. 2013) rely upon (Sakamoto et al. 2017). Incomplete fossils with missing morphological data have been shown to decrease the accuracy of inferred phylogenies (Guillerme and Cooper 2016; Vernygora et al. 2020), but this effect is lessened either when fossil taxa are scored alongside extant taxa and coding more morphological characters (Guillerme and Cooper 2016), or when increasing the number of included taxa in the analysis (Vernygora et al. 2020). The most straightforward way to minimize the negative effects of missing fossil morphological data on inferring evolutionary relationships is by utilizing the most complete and best-preserved fossil specimens. Most animal and plant fossil records, however, are made up of fragmentary remains and disarticulated parts (Crane et al. 2004; Brocklehurst et al. 2012; Dean et al. 2016), and by focusing primarily on complete specimens for phylogenetic analyses, the majority of extinct biodiversity and available fossil data in natural history collections is often excluded. Consequently, important fossil taxa known from fragmentary material remain underutilized in phylogenetic analyses, and we are left with considerable uncertainty in the evolutionary relationships of most known fossil organisms, which obscures our understanding of major evolutionary patterns in earth history (Sansom et al. 2010; Dornburg et al. 2015; Sansom 2015). Maximizing the vast amount of evolutionary information available in fossil collections necessitates a quantitative characterization of the biases present in this record. Furthermore, if we 76 wish to accurately assess the evolutionary relationships of incompletely preserved fossil specimens, we need to know whether the phylogenetic data preserved in these incomplete samples are reliable and consistent. I compiled a large dataset from natural history collections (6,585 specimens; 14,417 skeletal elements) to characterize skeletal representation bias in the extensive and diverse fossil record of squamates (lizards, snakes, amphisbaenians, and mosasaurs). I then apply parsimony- and model-based estimates of phylogenetic signal to test a major question fundamental to paleobiology: does the observed fossil record contain reliable phylogenetic information? 4.2. Materials and Methods 4.2.1. Sampling the Fossil Squamate Skeleton in Natural History Collections Despite their biases, natural history collections are the most data-rich record of the evolutionary history of squamates and are the basis for all morphological and most occurrence- based analyses of their fossil record. Although natural history collections have been used to assess the nature of bias and asymmetrical preservation in the squamate fossil record, these assessments are either limited to general observations (Nydam 2013; Rage 2013), or restricted taxonomically to mosasaurs (Driscoll et al. 2019). In this study, I quantify which regions of the squamate skeleton are more prevalent in natural history collections, and by extension, their observed fossil record. To understand which regions of the fossil squamate skeleton appear more frequently in museum collections, I divided the skeleton into seven discrete regions: 1) Jaws and palatal bones in the skull (all bones in the mandible, premaxilla, maxilla, vomer, palatine, pterygoid, and teeth); 2) posterior cranial bones (e.g., nasal, frontal, parietal, jugal, quadrate, braincase, etc.); 3) axial elements (i.e., vertebrae and ribs); 4) pectoral girdle; 5) pelvic girdle; 6) appendicular 77 elements; 7) dermal elements (Fig. 1, Supplementary Figure S1). Using these criteria, I sampled for the number of occurrences of fossil squamate skeletal elements belonging to each region. I surveyed 6,585 fossil squamate specimens and tallied 14,417 occurrences of individual skeletal elements across three major fossil squamate body plans: giant, fully aquatic/marine squamates (mosasaurs); small to medium-sized, four-limbed, terrestrial lizards; and small to medium-sized, limb-reduced/limbless squamates (e.g., snakes, amphisbaenians). The surveyed specimens range in age from the Late Jurassic to the Late Pleistocene (Fig. 2A). This study used in-person observations of fossil squamate collections, and surveyed readily-available digital collections databases. In-person sampling (Institutions: American Museum of Natural History (AMNH), New York, New York, United States of America; Denver Museum of Nature & Science (DMNH), Denver, Colorado, United States of America; Yale Peabody Museum of Natural History (YPM), New Haven, Connecticut, United States of America) was carried out by identifying squamate fossils to the lowest taxonomic level, and with as specific anatomical terminology as possible. Taphonomic bias and preservation mode played key roles in the precision of taxon identification and anatomical assignment. Incomplete specimens for which not enough diagnostic information was preserved were often restricted to identification at order/suborder/family taxonomic levels, using generalized anatomical terminology (e.g., “partial jaw bone”, “trunk vertebra”, “metapodial”). More complete specimens could be identified at Genus/Species taxonomic levels, with specific anatomical terminology (e.g., “anterior right maxilla”, “proximal left femur”, etc.). To broadly characterize fossil squamate morphological data available in museum collections globally, I sampled online electronic databases from 6 institutions on 3 continents (Institute for Vertebrate Paleontology and Paleoanthropology (IVPP), Beijing, China; Natural 78 History Museum London (NHMUK), London, United Kingdom; Natural History Museum of Los Angeles County (LACM), Los Angeles, California, United States of America; The Smithsonian National Museum of Natural History (USNM), Washington, D.C., United States of America; Washington, D.C.; University of Florida Museum of Natural History (UFMNH), Gainesville, Florida, United States of America; Yale Peabody Museum of Natural History (YPM), New Haven, Connecticut, United States of America). The criteria for selecting these institutions was dependent on readily-available digital vertebrate paleontology collections databases on the institution’s website, with collections data that could be downloaded as .csv files or efficiently converted to a dataframe. The compilation of each dataframe was achieved on each institution’s website by a simple keyword search for “Squamata” in the taxonomy category. An example of this workflow is given in Supplementary Figure S2, using YPM’s website. Once the dataframe was downloaded, I utilized the catalogued specimen labels to discern which elements of the fossil squamate skeleton were included under a given catalogue number. This was accomplished using keyword searches (command/control+F) for each bone in the squamate skeleton (Supplementary Data S1-S14) in Microsoft Excel. Because multiple skeletal elements are frequently included under a single specimen catalogue number, my search criterion was “number of occurrences” of a skeletal element on the specimen labels, rather than the number of individual elements with a catalogue number. If specific counts for a given skeletal element was indicated on the specimen label (e.g., vertebra [x35]), that counted number was included in the total specimens from the collection. If no count was included on a specimen label, then I counted the occurrence of that skeletal element as a single occurrence. I designed the keyword searches to be as inclusive as possible regarding the anatomical language on each specimen label. Some specimens had thorough anatomical descriptions (e.g., posterior portion of 79 the left maxilla), while others were more general (e.g., “jaw fragment”). Regardless of level of detail on the label, if an element could be assigned to one of the seven anatomical regions I designated, I included it in the survey. Because the anatomical binning of phylogenetic characters for the assessments of phylogenetic signal uses the same seven anatomical regions (see below), this allowed me to include the specimen data with less specific labels in the characterization of bias in museum collections. 4.2.2. Measurement of Phylogenetic Signal In this survey of fossil squamate collections, one would expect that taphonomic and anthropogenic sampling biases will lead to some regions of the skeleton being more frequently represented compared to others (Supplementary Figure S3). In a phylogenetic context, this imbalanced representation of the skeleton may not align with the regions of the skeleton that are more heavily emphasized for morphological character selection in phylogenetic analyses. For example, the vertebrate skull is usually the most heavily-emphasized and character-dense skeletal region in phylogenetic analyses, whereas other regions of the skeleton, such as the spinal column or appendicular regions, are comparatively less emphasized and less character dense. If a group of vertebrates has a fossil record in which few or no skull material is preserved/collected, and instead is mostly represented by vertebrae, then the vertebrae are “overrepresented”, given the smaller number of phylogenetic characters they can be scored for. Conversely, the skull material, or lack thereof, is “underrepresented” in the fossil record, given the larger quantity of phylogenetic characters they can be scored for. In this scenario, the accuracy of phylogenetic analyses for this fossil group is dependent on the fidelity of the “overrepresented” vertebral character evolution to the hypothesized topology of that group. To make sure these characters are reliable for reconstructing phylogeny, it is necessary to use measurements of phylogenetic signal 80 to assess the quality of morphological character data both in “overrepresented” and “underrepresented” parts of the skeleton made available by the biased fossil record. The presence of competing morphology-based hypotheses for the higher-level evolutionary relationships of squamates (Gauthier et al. 2012, Simões et al. 2018) represents an opportunity to explore patterns of phylogenetic signal in the extensive fossil record (>242 million years, Simões et al. 2018) of a major component of the modern vertebrate fauna (>11,182 extant species, Uetz et al. 2021). Broadly, phylogenetic signal describes the tendency of closely related species to resemble each other in a given trait, as the result of shared evolutionary history (Pagel 1999; Blomberg et al. 2003; Borges et al. 2019). Phylogenetic signal is measured by tracking how closely the evolution of a character trait aligns with a given evolutionary hypothesis. I used two topologically incongruent morphological phylogenetic datasets, one from Gauthier et al. (2012) (GEA) and the other from Simões et al. (2018) (SEA), to assess the reliability of phylogenetic data present in the squamate fossil record. The GEA and SEA character matrices and .tre files of the strict consensus trees were downloaded from a publicly-available phylogenetic database on G. T. Lloyd’s website (http://www.graemetlloyd.com). The time-calibrated Bayesian Majority-Rule Consensus tree from the SEA dataset used for calculation of the d-Statistic was obtained upon request from T. R. Simões. All phylogenetic datasets used in this study are available in Supplementary Data S15- S18, S24-S29. To minimize the impact of highly incomplete fossils on estimates of phylogenetic signal, fossil taxa were removed from the GEA and SEA datasets using Mesquite (Maddison and Maddison 2018) and the drop.tip function in the {ape} package (Paradis and Schliep 2019) in R (R Core Team 2013), and only the extant taxa included in GEA and SEA datasets were considered herein. To effectively calculate measurements of character evolution and 81 phylogenetic signal, morphological characters that remained in a constant state (i.e., zero changes across the entire evolutionary tree with dropped fossil taxa) were removed prior to carrying out analyses. 4.2.2.a. Parsimony-based Phylogenetic Signal.–– To assess phylogenetic signal of skeletal elements in a parsimony-based framework, I calculated character Consistency Index (CI, Kluge and Farris 1969) and Retention Index (RI, Farris 1989) values corresponding to the seven anatomical bins utilized in my sampling of fossil squamate collections. I used these values to measure differences in homoplasy (CI) and retained synapomorphy (RI) for characters corresponding to the seven regions of the fossil squamate skeleton. Individual CI and RI values for the 572 pruned GEA characters and 222 pruned SEA characters were calculated using the {ape}, {TreeSearch} (Smith 2018), and {phangorn} (Schliep 2011) packages in R (Supplementary Data S19-S22). The characters were binned according to anatomical region in my sampling of museum collections (Fig.1, Supplementary Figure S1), and the distributions (see Supplementary Figure S4, S5) were then compared to one another using two non- parametric statistical tests: 1) Mann-Whitney U-Test; 2) Kolmogorov-Smirnov Test (Supplementary Data S23). Because I performed multiple statistical comparisons of CI and RI values across all anatomical regions (GEA: n = 37; SEA: n = 29), statistical tests were run using a Bonferroni correction on the a value. Additionally, because the GEA and SEA datasets contain 30 overlapping operational taxonomic units (OTU’s), I swapped the character matrices (Supplementary Data S76-S77) and their corresponding topologies (Supplementary Data S80- S81) to compare phylogenetic signal of the same character partitions using a fundamentally different topology (Supplementary Figure S6-S8). 82 4.2.2.b. Model-based Phylogenetic Signal.–– Recently, the d-Statistic (Borges et al. 2019) was developed as a means of utilizing model-based phylogenetic comparative methods to assess phylogenetic signal within categorical character data, and has been recently applied in addressing paleobiological questions (e.g., Deline et al. 2020). Calculating the d-Statistic for a given morphological character relies on ancestral character state probabilities at each node in a phylogeny. The model operates under the expectation that the better a phylogeny is associated with a given trait, the better it is able to infer ancestral states with minimal uncertainty. The ancestral state probabilities simulate “entropy” at a given node: the higher the uncertainty in a given character state (i.e., less phylogenetic signal), the higher the “entropy” value at that node (see Borges et al. 2019 for further explanation). d is a measurement of the ratio of the distribution of higher “entropy” values to the distribution of lower “entropy” values for a given character across all nodes in a phylogeny. d is higher when the distribution of “entropies” favors lower values (i.e., less ancestral state uncertainty) over higher values (i.e., more ancestral state uncertainty). Ancestral states for both the GEA and SEA characters were reconstructed using the R wrapper BTW (randigriffin.com/projects/btw) for the Bayestraits (Meade and Pagel 2016) program (Supplementary Figure S9). Trees for the GEA dataset did not have branch lengths, so I time-calibrated the tree with a dataset of all fossil ages using the Minimum Branch Length (MBL) method (Laurin 2004). I dated 78 internal nodes dated using a previously-published time- calibrated version of the GEA tree (Pyron 2017) and minimum branch lengths of 3, 5, and 7 million years with the BinTimePaleoPhy function in the R package {paleotree} (Bapst 2012). I initially ran these analyses using all non-constant characters in the GEA and SEA datasets, as I had done for my parsimony-based measurements of phylogenetic signal (Supplementary Figure S10-S13). However, unlike the parsimony-based measurements, I 83 found a strong negative relationship between the percentage of missing/non-applicable scores and the d-Statistic value for a given character (higher percentage of missing/non-applicable scores correlates to lower d-Statistic values) (Supplementary Figure S14-S16, Supplementary Discussion, Supplementary Data S47). For the analyses presented herein, I only considered characters for which all taxa were scored. Additionally, the extreme morphological disparities between limbed and limbless squamate taxa contributed to a large amount of missing/non- applicable scorings when considering the two body plans together. Because of this, I ran the analyses separately for limbed and limbless squamate taxa for the GEA dataset (Supplementary Figure S17-S19, S21), and limbed squamates for the SEA dataset (Supplementary Figure S20). Because there are only 8 extant legless taxa in the SEA dataset, I could not analyze d-Statistic values for this subset of data; d-Statistic model sensitivity drastically decreases using < 20 taxa (Borges et al. 2019). I used the drop.tip function in the {ape} package (Paradis and Schliep 2019) in R (R Core Team 2013) to remove the appropriate taxa for each analysis. I then calculated node probabilities for each character state for the non-constant, completely scored GEA characters and SEA characters. The d-Statistic was then calculated for each character using the set of resulting node probabilities for the GEA and SEA datasets for each character using the R script from Borges et al. (2019) (GitHub branch: mrborges23/delta_statistic) (Supplementary Data S30-S45, S52- S71). Bootstrap tests for differences between median d-Statistic values among anatomical distributions of phylogenetic characters were carried out using 10,000 samples with replacement in R (Supplementary Data S46). Because I performed multiple comparisons of d-Statistic values across all anatomical regions (GEA limbed: n = 37; SEA limbed: n = 29; GEA limbless: n = 11; GEA snakes: n = 16), bootstrap tests were run using a Bonferroni correction on the a 84 value. Similarly to the parsimony-based assessments of phylogenetic signal, I swapped character matrices (Supplementary Data S78-S79) and topologies (Supplementary Data S80-S81) using 23 overlapping legged OTU’s among the GEA and SEA datasets. Code to repeat parsimony- and model-based analyses of phylogenetic signal are available at the GitHub branch chwoolle/PhylogeneticSignal. 4.3. Results 4.3.1. Characterizing Bias in the Squamate Fossil Record Similar patterns of skeletal region representation are found in the fossil record of the three major squamate body plans (Fig. 2 B-D). Among mosasaurs (Fig. 2B), 83.41% of the observed fossil elements came from the axial (65.47%, n = 2,544) and jaws + palatal (17.94%, n = 697) regions of the skeleton. Among lizards (Fig. 2C), 77.8% of the observed fossil elements came from the axial (14.77%, n =1050) and jaws + palatal (63.03%, n = 4,308) regions of the skeleton. The overwhelming majority (96.95%, n = 2,983) of fossil legless squamate skeletal elements (Fig. 2D) belong to the axial region of the skeleton, whereas jaws + palatal elements (2.67%, n = 82) make up almost all of the remaining occurrences. These results reveal that the majority of fossil squamate morphological data (84.28%, Fig. S3A) in museum collections is from the axial and jaws + palatal regions of the skeleton, whereas other regions of the skeleton (posterior cranial, dermal, pectoral and pelvic girdle, appendicular elements) do not occur as frequently. Additionally, notable discrepancies in morphological data are present between specimens sampled in-person and specimens sampled using electronic collections databases, with in-person sampling yielding a higher proportion of dermal and appendicular skeletal elements than sampled in electronic databases (Fig. S3A). These differences emphasize the 85 importance of increased physical access to natural history collections, and caution against overreliance on databases as a panacea for paleobiological analyses (See Supplementary Text). I interpret the distribution of fossil squamate skeletal data using the following terminology: the jaws + palatal and axial regions of the fossil squamate skeleton are comparatively “overrepresented” in natural history collections, whereas the posterior cranial region of the skull, pectoral and pelvic girdles, appendicular elements, and dermal elements are comparatively “underrepresented”. For example, the low occurrence of squamate posterior cranial skeletal elements in collections (4.74% of skeletal element occurrences) contrasts with an outsized proportion of morphological characters sourced from posterior cranial skeletal elements (43.61% and 34.29%, respectively, Supplementary Figure S3B) in the GEA and SEA datasets. Therefore, in both raw numbers and within the context of phylogenetic data, the posterior cranial region of the skull is underrepresented in the squamate fossil record. Similarly, the axial region of the skeleton, which makes up the largest portion of fossil skeletal data (46.79%), but a small portion of phylogenetic characters in the GEA and SEA datasets (4.10% and 14.99%, respectively), is overrepresented in the squamate fossil record. This decoupling of skeletal partitions represented in fossil data from the partitions emphasized in phylogenetic datasets necessitates a test of whether overrepresented regions in the fossil record contain as much, more, or less phylogenetically informative character data than underrepresented regions. 4.3.2. Analyses of phylogenetic signal 4.3.2.a. Parsimony-based Assessments of Phylogenetic Signal.–– Overall, I found no statistically significant difference between the distributions of CI and RI values (Fig. 3B,C; 3E,F) among characters corresponding to either overrepresented or underrepresented skeletal regions (Mann-Whitney U, Kolmogorov-Smirnov tests, all p-values >a, Supplementary Data 86 S23). If we parse out the character CI and RI distribution per squamate anatomical bin (Supplementary Figure S4, S5; Supplementary Data S15-S23), we observe that distribution shapes and mean CI values (GEA dataset) and RI values (GEA dataset) of characters corresponding to the pectoral girdle are statistically significantly different from other regions the skeleton. Among characters in the other anatomical bins (Jaws + Palate, Axial, Posterior Cranial, Pelvic, Appendicular, Dermal, Other characters), the amount of homoplasy and retained synapomorphy of characters is not significantly different when compared to one another in both GEA and SEA datasets (Supplementary Data S23). With character matrices and topologies swapped (Supplementary Figure S6), I found no statistically significant differences in median values and distribution shapes of overrepresented and underrepresented skeletal regions at-large (Mann-Whitney U, Kolmogorov-Smirnov tests, all p-values >a, Supplementary Data S23). However, when we parse out the GEA matrix vs. SEA topology results by anatomical region (Supplementary Figure S7), we observe statistically significant differences in median value and distribution shape of the RI values of characters corresponding to the pectoral girdle and appendicular elements are statistically significantly different from other regions the skeleton (Supplementary Data S23). CI values of GEA matrix vs. SEA topology characters corresponding to the pelvic girdle were statistically significantly different than other regions of the skeleton (Supplementary Data S23). For the SEA matrix vs. GEA topology, there were no statistically significant differences among any of the anatomical regions (all p-values >a, Supplementary Data S23). 4.3.2.b. Model-based Assessments of Phylogenetic Signal.–– For both the GEA and SEA datasets, characters with 0% missing data that correspond to overrepresented regions of the squamate skeleton in the fossil record exhibit: 1) similar overall variation in d-Statistic values, 87 and 2) similar median d-Statistic values to characters with 0% missing data that correspond to underrepresented regions of the squamate skeleton in the fossil record (Fig. 4, 5). Two-sample bootstrap tests comparing 10,000 re-samples with replacement of the median d-Statistic values of overrepresented and underrepresented characters, using a Bonferroni-corrected a (Supplementary dataset S46), reveal that the differences are not statistically significant, regardless of evolutionary hypothesis (GEA limbed: p=0.4275; SEA limbed: p=0.6978; GEA limbless: p=0.1997; GEA snakes: p=0.475; Supplementary dataset S46). Sensitivity analyses using each of the minimum branch lengths were run to account for branch length uncertainty in the GEA dataset, though results were broadly the same (Supplementary Figure S17-S19, Supplementary Data S30-S45). The SEA topology was already time-calibrated (Simões et al. 2018), therefore sensitivity analyses concerning branch lengths were not run for that topology. Additionally, to assess the stability of these results under different model parameters, I ran a number of additional sensitivity analyses using different prior distributions on character transition rates (U:0-0.001, U:0-0.1, U:0-1.0). Results were largely insensitive to differences in model parameters (Supplementary Figure S17-S20). When I swapped the GEA and SEA character matrices with their topologies (overlapping limbed squamate OTU’s only), I found no statistically significant differences in the median d-Statistic values between any of the anatomical regions (all p-values >a, Supplementary Data S46, Supplementary Figure S26-S28). 4.4. Discussion 4.4.1. Biases in the Squamate Fossil Record Considering that jaw + palatal bones in the skull and the axial region of the squamate skeleton contain dozens to hundreds of individual elements (e.g., vertebrae, ribs, isolated teeth), it is unsurprising that we see the highest raw numbers of skeletal elements from these regions 88 among the fossil specimens surveyed (Fig. 2 B-D, Supplementary Figure S3A). In fact, the relative occurrences of all seven skeletal regions in the fossil records of mosasaurs (Fig. 2B) and legless squamates (Fig. 2D), appear to superficially coincide with the number of potentially “fossilizable” skeletal elements in these animals. The major anomaly, from a preservation/collecting perspective, comes from the fossil record of lizards, which disproportionately favors the jaw + palatal region of the skull (Fig. 2C). This may be due to the fact that the enamel of teeth are more resilient to taphonomic factors, and that isolated lizard jaws can generally be easily distinguished from other small vertebrate teeth and tooth-bearing elements (combination of pleurodonty and heterodonty). As a result, based on raw numbers, the only clearly discernible taphonomic/collecting bias in the squamate fossil record comes from the portion pertaining to lizards. Future work utilizing established fossil completeness metrics (Brocklehurst et al. 2012; Dean et al. 2016; Driscoll et al. 2019; Woolley et al. 2021) would allow us to further characterize the taphonomic and/or collecting biases that lead to the distribution of the fossil squamate skeleton observed herein. If we are to consider squamate evolution as a whole, and our ability to place fossil squamates into broad, higher-level phylogenies alongside extant taxa, then the squamate fossil record is biased against the region of the skeleton containing the highest amount of phylogenetic data (the posterior cranial region of the skull, 43.61% of GEA characters and 34.29% of SEA characters, Supplementary Figure S3B). Additionally, this survey shows that the majority of morphological phylogenetic characters available to score (GEA: 67.87%; SEA: 56.48%, Supplementary Figure S3B) belong in squamate skeletal regions that are underrepresented in museum collections. This means that even though taphonomic and collecting biases largely align with the material in the skeleton available to fossilize (with the exception of fossil lizards), the 89 observed record of fossil squamates is still biased against the regions of the skeleton that contain the majority of phylogenetic characters. Because the squamate fossil record is clearly missing a large quantity of useful phylogenetic data, it is imperative to assess the quality of the data that remains in characters associated with jaws + palatal elements, and axial elements. 4.4.2. Homoplasy and Retained Synapomorphy in the Fossil Record Results from the comparisons of CI and RI distributions among the GEA and SEA datasets demonstrate that overrepresented phylogenetic character data from the squamate fossil record are not any more likely to provide misleading evidence of phylogenetic relationships than character data from the rest of the skeleton. The lack of a significant difference in observed homoplasy between characters more prevalent in the squamate fossil record suggests that the phylogenetic placements of incomplete and fragmentary fossil taxa are neither more, nor less reflective of evolutionary convergence than those of more complete, extant taxa. Similarly, the lack of significant difference in retained synapomorphy among characters in overrepresented versus underrepresented fossil squamate skeletal elements suggests that the phylogenetic placements of fragmentary fossil taxa are neither more, nor less reflective of shared derived character states than more complete, extant taxa. Critically, this parsimony-based result is recovered regardless of hypothesis of squamate higher-level evolutionary relationships. It is unclear what the exact cause is behind the lower CI and RI values for characters sourced from the pectoral girdle in the GEA phylogenetic dataset (Supplementary Figure S4). Comparisons between CI/RI value and percentage of missing data per character (Supplementary Text, Supplementary data S47) showed no meaningful relationship, unlike the model-based measurement of phylogenetic signal. This suggests that missing/non-applicable character data does not account for the patterns in CI/RI values among pectoral characters in the 90 GEA dataset. It is possible that major ecomorphological transitions in squamate evolution, such as limb loss and/or specialized pectoral/limb morphologies may play a role in these differences. Alternatively, lower overall sample sizes of phylogenetic characters scored from this skeletal region (Supplementary Figure S4-S5) could factor into these CI/RI distribution differences. Regardless of cause, the lack of significant differences in the distributions of overrepresented and underrepresented CI/RI values in the large samples sizes of phylogenetic characters in the skull (jaws + palatal and posterior cranial regions) appear to be the most influential on these results. These results are generally consistent even when swapping character matrices and topologies (Supplementary Figure S6), with the exception of the RI values of GEA appendicular characters mapped onto the SEA topology (Supplementary Figure S7, Supplementary Data S23). The higher median RI value and higher variation in the range of RI values in the GEA appendicular region (Supplementary Figure S4) are eradicated when mapped onto the SEA topology (Supplementary Figure S7). This could be due to the possibility that GEA appendicular characters demonstrate high support for crownward nodes on the GEA topology, but because of the fundamental differences in evolutionary hypotheses, the characters do not support major nodes on the SEA tree. Further tests, including running separate phylogenetic analyses using each anatomical partition (e.g., Wencker et al. 2021), could be used in the future to understand the causes behind these differences in more detail. 4.4.3. Model-based Analyses of Phylogenetic Signal Among GEA and SEA characters with no missing data, regions of the squamate skeleton that are underrepresented in the fossil record exhibit similar levels of median phylogenetic signal to overrepresented regions as measured by the d-Statistic. This is true when we consider only legged squamate taxa (Fig. 4-5), only legless squamate taxa (Fig. 6), and snake taxa in the GEA 91 dataset (Supplementary Figure S21). By running separate analyses of legged taxa and legless taxa, I was able to consider a portion of characters corresponding to the pectoral girdle, pelvic girdle, and appendicular elements in legged squamates. However, even though I was able to survey representative characters for each of the seven anatomical regions, the strong negative correlation of missing data to d-Statistic values meant that I could only include roughly one-third of the total amount of characters (195 GEA characters, or 31.97% of total; 126 SEA characters, or 36.31% of total). In the absence of an appropriate benchmark study stating the minimum number of characters that can be used for the d-Statistic, it is difficult to tell how much the estimates of phylogenetic signal using the d-Statistic are impacted by low character sample size. However, the d-Statistic results are consistent with the parsimony-based results, which: 1) are derived from a much larger sample of characters (572 GEA characters, or 93.77% of total; 222 SEA characters, or 63.97% of total), and 2) have no discernable relationship with the amount of missing data (Supplementary data S47). This suggests that smaller character sample sizes may not affect the sensitivity of the d-Statistic analyses as much as, for example, the number of included taxa (Borges et al. 2019). Further work to more rigorously assess the effect of small sample sizes on the d-Statistic is needed, but at present, I conclude that the analyses in this study are still an appropriate use of the method. For both the GEA and SEA datasets, appendicular characters showcased the highest median d-Statistic value, in addition to an interquartile range with the highest d-Statistic values, among all anatomical bins that contained >2 characters (Fig. 5; Supplementary Figure S22, S23, S27). Possible explanations for this pattern among appendicular characters vary according to phylogenetic dataset. For the GEA dataset, a potential explanation for the high median d- Statistic values in appendicular characters has to do with the unique limb structure of the 92 chamaeleonid taxa (Brookesia brygooi and Chamaeleo laevigatus) that were scored differently from all other limbed taxa. Because chamaeleonids are monophyletic in the GEA hypothesis, this results in higher d-Statistic values for the appendicular character bin, even though the characters do not illuminate relationships for any group of lizards beyond Chamaeleonidae. The character selection and taxa used in the SEA dataset are different, and the one sampled chamaeleonid taxon (Trioceros jacksonii) does not appear to be influencing d-Statistic as strongly as the chamaeleonids in the GEA dataset. However, for both datasets, there are unique differences between the squamate limb and the limb of the outgroup taxon, Sphenodon punctatus (e.g., the presence of epiphyses on long bones), that polarize the characters and result in high d-Statistic values, but are not necessarily informative on the interrelationships among limbed squamate taxa. In sum, the higher phylogenetic signal for appendicular characters is probably driven by the monophyly of small subset of unique taxa (Chamaeleonidae), as well as the ingroup/outgroup distinction among all squamates and S. punctatus. Even with the character matrices and topologies swapped (Supplementary Figure S27- S28), appendicular characters exhibit the highest median d-Statistic values and an interquartile range with the highest d-Statistic values among all anatomical regions. Why this differs from the appendicular RI values is unclear, especially given the median RI value of GEA appendicular characters lowered significantly when mapped onto the SEA topology (Supplementary Figure S7B). It is possible that the relatively smaller sample size of GEA characters in the appendicular region for the d-Statistic analyses excluded key characters that contributed to the lower median RI value and greater interquartile range. These conflicting results could also demonstrate greater plasticity in squamate limb morphology, where, apart from a few clades (e.g., Chamaeleonidae), 93 limb morphological character evolution carries lower phylogenetic signal across the squamate tree of life. d-Statistic values for characters associated with axial region of the squamate skeleton have variable distributions according to dataset and taxon subsets used. For both the GEA and SEA datasets in which only legged taxa were sampled, the axial characters have the lowest (SEA) or third-lowest (GEA) median d-Statistic value out of all sampled anatomical regions (Fig. 5; Supplementary Figure S22-S23; Supplementary Figure S27-S28). The same results hold for the swapped character matrices and topologies (Supplementary Figure S27-S28). For the GEA dataset in which only snakes were sampled, the axial characters had higher median d- Statistic values than other regions (Supplementary Figure S25). This suggests that, at least for the GEA dataset, axial characters are comparably more phylogenetically informative for snake taxa than they are for legged taxa or all legless taxa within the dataset. Within the context of the fossil record of snakes and other legless squamates (Fig. 2D), in which the vast majority of identified elements are from the axial region of the skeleton, this adds confidence to our ability to include incomplete fossil snakes into broader phylogenetic analyses. As was the case with the parsimony-based measurements of phylogenetic signal, the anatomical bins with the largest sampling of characters (jaws + palatal and posterior cranial elements of the skull) appear to be influencing the results of these statistical comparisons the most. Bootstrap tests (Supplementary data S46) indicate that there is no statistically significant difference between the median d-Statistic value of jaws + palatal and posterior cranial elements of the skull (all p-values > a), which correspond to overrepresented and underrepresented regions of the fossil squamate skeleton, respectively. This means that jaws + palatal and posterior cranial elements of the skull, which happen to be the most character-rich regions of the squamate 94 skeleton, showcase levels of phylogenetic signal that are consistent with one another (Fig. 5; Supplementary Figure S22-S25, S27-S28). It is important to consider this result alongside the observed fossil record of lizards (Fig. 2C; Nydam 2013; Rage 2013), which disproportionately preserves jaws + palatal elements of the skull (in particular, dentaries and maxillae). By demonstrating that these skeletal regions retain similar levels of phylogenetic signal as posterior cranial elements of the skull and other underrepresented regions of the fossil squamate skeleton, we can be more confident that including incomplete fossil lizard taxa in phylogenetic analyses won’t provide misleading evidence of evolutionary relationships. 4.5. A biased fossil record contains reliable phylogenetic data The arrival at similar assessments of phylogenetic signal using two non-independent but distinct phylogenetic datasets (GEA and SEA) gives me confidence that I am describing an actual natural phenomenon in the preservation of fossil data. The parsimony-based and model- based analyses show that the parts of the squamate skeleton most ubiquitously preserved and collected in the fossil record (jaws + palatal bones, vertebrae, and ribs) retain the same level of phylogenetic signal as other parts of the skeleton. Critically, these results are recovered regardless of hypothesis of squamate higher-level evolutionary relationships. This joint assessment of bias and phylogenetic signal in this sample of morphological data adds confidence to our ability to accurately infer the evolutionary relationships of fossil organisms that preserve disarticulated parts. 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B) Posterior Cranial elements (inset: YPM (unnumbered), partial frontal). C) Dermal elements (osteoderms) (inset: DMNH EPV.119455, Anguidae osteoderm, from Woolley, Smith & Sertich (2020). D) Axial elements (inset: UU MAA 7173, Ophisaurus partial trunk vertebra, from Georgalis et al. (2019). E) Pectoral Girdle (inset: YPM 3230, Polyglyphanodon sternbergi scapulocoracoid) F) Appendicular elements (inset: YPM 3230, P. sternbergi forelimb) G) Pelvic Girdle (inset: YPM 3230, P. sternbergi incomplete pelvis). 101 Figure 2. Summary of sampled squamate collections (combined in-person and electronic databases), divided by schematic diagrams of predominant fossil squamate body plans. A) Sampled intervals in geologic time for mosasaurs, lizards, and legless squamates. Silhouettes traced from publicly-available renderings at Phylopic.org. B) Distribution of skeletal elements assigned to taxa within Mosasauria. Skeletal schematic drawing of LACM 128319, Platecarpus tympanicus, Smoky Hill Chalk Member (Niobrara Formation), late Santonian–earliest Campanian, Kansas; adapted from Konishi et al. (2012). C) Distribution of skeletal elements assigned to squamates excluding mosasaurs and legless squamates (i.e., lizards). Skeletal line drawing of YPM 3230, an articulated skeleton of P. sternbergi, missing the tail, from the Maastrichtian North Horn Formation, Utah, USA. D) Distribution of skeletal elements assigned to legless squamates. Skeletal line drawing of SMFME 11332a Palaeopython fischeri, Middle Eocene of Messel, Germany; adapted from Smith & Scanferla (2016). 102 Figure 3. Summary of parsimony-based measurements of phylogenetic signal in the squamate fossil record used in this study. A) Hypothesis of higher-level squamate relationships according to Gauthier et al. (2012) (GEA). Silhouettes traced from publicly-available renderings at Phylopic.org. Silhouettes with highlighted outlines indicate clades with notably different positions in the two hypotheses presented herein. B) Distribution of CI values for GEA characters corresponding to overrepresented skeletal elements in the squamate fossil record (See inset, center: overrepresented and underrepresented fossil skeletal regions mapped onto a schematic diagram of U. stansburiana) and all underrepresented skeletal elements in the squamate fossil record. C) Distribution of RI values for same GEA character bins as in (B). D) Hypothesis of higher-level squamate relationships according to Simões et al. (2018) (SEA). E) Distribution of CI values of SEA characters. F) Distribution of RI values of SEA characters. 103 Figure 4. Distributions of d-Statistic for the pruned GEA and SEA legged squamate character dataset (prior on transition rates for ancestral node probability calculations = 0.01). Inset: overrepresented and underrepresented fossil skeletal regions mapped onto a schematic diagram of U. stansburiana. A) Comparative diagram of the distribution of d-values between GEA characters (time-calibrated fossil tips + 78 internal nodes with minimum branch lengths of 5 million years) corresponding to overrepresented (green) and underrepresented (blue) fossil squamate skeletal elements. B) Comparative diagram of the distribution of d-values between SEA characters corresponding to overrepresented (green) and underrepresented (blue) fossil squamate skeletal elements. 104 Figure 5. Distributions of d-Statistic among anatomical bins for the pruned GEA and SEA legged squamate character dataset (prior on transition rates for ancestral node probability calculations = 0.01). Inset, left: Schematic diagram of an example squamate skeleton (modeled after Uta stansburiana), with colorized anatomical regions used in this study. A) Summary of distributions of d-Statistic values for characters with 0% missing data in the GEA dataset using only limbed squamate taxa. B) Summary of distributions of d-Statistic values for characters with 0% missing data in the SEA dataset, using only limbed squamate taxa. 105 Figure 6. Distributions of d-Statistic for the pruned GEA legless squamate character dataset (prior on transition rates for ancestral node probability calculations = 0.01). Inset, left: overrepresented and underrepresented fossil skeletal regions mapped onto a schematic diagram of Crotalus atrox. Right: Comparative diagram of the distribution of d-Statistic values between GEA characters (time-calibrated fossil tips with minimum branch lengths of 3 million years) corresponding to overrepresented (green) and underrepresented (blue) fossil squamate skeletal elements. 106 4S Supplementary Material for Chapter 4 Supplementary Discussion Discrepancies between in-person and electronic collections database sampling. We observed several differences between fossil squamate specimens sampled in-person and via electronic collections databases (Fig. S2A). In-person sampling yielded a higher proportion of dermal and appendicular skeletal elements than sampled in electronic databases (Fig. S2A). One possible reason for the differences in observed dermal skeletal element appearances could be that squamate osteoderms, when preserved, are generally extremely numerous and tedious for collections staff/volunteers to count, and as a result, they are generally batch-catalogued with the label “osteoderms”, or ”numerous osteoderms”. While I was able to count the individual osteoderms we sampled in-person, I was not able to count osteoderms in the electronic collections database sample, because this sampling technique relied solely on labels associated with the catalogued specimen. This same possible explanation can be applied to the numerous, small bones that make up the squamate manus and pes (difficult to identify and tedious to count), that lead to the discrepancy between in-person and electronic samples of appendicular elements. These highlighted discrepancies emphasize the importance of increasing in-person access to organized, curated natural history collections, and caution against an exclusive reliance on electronic databases as unbiased sources of natural history data. In addressing broad, regional and global paleobiological questions, in-person and electronic sampling both have limitations, and both were used in this study to account for each method’s shortcomings. Supplementary Materials and Methods Institutions sampled: American Museum of Natural History (AMNH), New York, New York, United States of America; Denver Museum of Nature & Science (DMNH), Denver, Colorado, 107 United States of America; Institute for Vertebrate Paleontology and Paleoanthropology (IVPP), Beijing, China; Natural History Museum London (NHMUK), London, United Kingdom; Natural History Museum of Los Angeles County (LACM), Los Angeles, California, United States of America; The Smithsonian National Museum of Natural History (USNM), Washington, D.C., United States of America; Washington, D.C.; University of Florida Museum of Natural History (UFMNH), Gainesville, Florida, United States of America; Yale Peabody Museum of Natural History (YPM), New Haven, Connecticut, United States of America. In-person sampling of fossil squamate collections. Taphonomic bias and preservation mode played key roles in the precision of taxon identification and anatomical assignment. Incomplete specimens for which not enough diagnostic information was preserved was often restricted to identification at order/suborder/family taxonomic levels, using generalized anatomical terminology (e.g., “partial jaw bone”, “trunk vertebra”, “metapodial”). More complete specimens could be identified at Genus/Species taxonomic levels, with specific anatomical terminology (e.g., “anterior right maxilla”, “proximal left femur”, etc.). In-person sampling has a clear advantage over digital collections databases in potential for comprehensive specimen examination: the specimens are physically present with the researcher, making all surficial details of a given fossil available for scrutiny. While in-person examination of fossil data is still arguably the most widely employed sampling method for fossil descriptions, there are important sources of bias within this method to consider. Examples of sources of bias for in-person sampling of fossil squamate morphological data include: 1) background knowledge/expertise of the researcher, 2) amount of time made available by a given institution 108 for a researcher to spend in a given collection, 3) potentially prohibitive financial limitations on the researcher visiting a collection (travel costs, housing/food costs, bench fees, etc.). All three of these sources of bias played a role during in-person surveys of the fossil squamate collections at the Denver Museum of Nature & Science (DMNS), Yale Peabody Museum of Natural History (YPM) and the American Museum of Natural History (AMNH). Time allotted at each institution (roughly 40 days at DMNS as a collections volunteer researcher; one week each at YPM and AMNH as a visiting researcher) resulted in different assessments of fossil squamate skeletal preservation (see supplementary data S12-S13). Additionally, these collections visits focused on Late Cretaceous terrestrial squamate collections from western North America, which covers a relatively small geographic range, a narrow range of depositional settings (terrestrial fluvial depositional settings), and only a narrow slice of time in the >242 million-year squamate fossil record. In order to rectify this sampling bias in-person, thousands of hours would need to be spent at dozens of institutions worldwide, which is extremely financially prohibitive and unrealistic. Electronic collections databases. My criteria for selecting the institutions included in this part of the survey was dependent on readily-available digital vertebrate palaeontology collections databases on the institution’s website, with collections data that could be downloaded as .csv files or efficiently converted to a dataframe The compilation of each dataframe was achieved on each institution’s website by a simple keyword search for “Squamata” in the taxonomy category. Once the dataframe of the squamate specimens and their corresponding information was downloaded, we utilized the catalogued specimen labels to discern which elements of the fossil squamate skeleton were included under a given catalogue number. This was accomplished using 109 keyword searches (command/control+F) for each bone in the squamate skeleton (Supplementary Data S1-S14) in Microsoft Excel. Because multiple skeletal elements are frequently included under a single specimen catalogue number, my search criterion was “number of occurrences” of a skeletal element on the specimen labels, rather than the number of individual elements with a catalogue number. If specific counts for a given skeletal element was indicated on the specimen label (e.g., vertebra (x35)), that counted number was included in the total specimens from the collection. If no count was included on a specimen label, then we counted the occurrence of that skeletal element as a single occurrence. We designed the keyword searches to be as inclusive as possible regarding the anatomical language on each specimen label. Some specimens had thorough anatomical descriptions (e.g., posterior portion of the left maxilla), while others were more general (e.g., “jaw fragment”). Regardless of level of detail on the label, if an element could be assigned to one of the seven anatomical regions we designated, we included it in the survey. Because my anatomical binning of phylogenetic characters for the assessments of phylogenetic signal uses the same seven anatomical regions (see below), this allowed us to include the specimen data with less specific labels in my characterization of bias in museum collections. Electronic collections databases, often freely-accessible and allowing for incorporation of more data than a typical research collections visit, are used herein to account for the above shortcomings of in-person collections sampling. However, it is important to acknowledge that the keyword searches of online fossil squamate collections performed herein are inherently biased for several non-insignificant reasons. First, the online collections databases themselves 110 are only partial representations of the entirety of the collection; each of the natural history museums sampled herein are actively digitizing their collections, and not every specimen in the collection has been made available online. Second, my inability to personally examine each specimen in the digital collection forces us to be dependent on the accuracy of the taxonomic and anatomical identifications on the specimen labels, most of which are not published and subject to peer review. Third, the lack of individual skeletal element counts on some specimen labels in this dataset (Supplementary Data S1-S14) means that these basic occurrence counts are underestimating the total number of skeletal elements in a given fossil squamate collection. Fourth, this survey only includes collections that have publicly-accessible online collections, and therefore we acknowledge that this excludes the majority of worldwide fossil squamate collections that do not have online digital counterparts. In spite of these limitations, this digital dataset still represents an important tool for estimating bias in the squamate fossil record, and is employed herein to account for limitations related to in-person sampling (see above). Consistency Index and Retention Index. To compare the phylogenetic information preserved in overrepresented vs. underrepresented skeletal elements in my sampling of the squamate fossil record, we employed two widely-used, parsimony-based metrics of homoplasy (Consistency Index, CI 1 ) and retained synapomorphy (Retention Index, RI 2 ). CI values for a given character across an evolutionary tree are calculated using Equation 1 below: 𝐶𝐼 = 𝑚 𝑠 Where 𝑚 is equal to the minimum number of state changes of a given character required parsimoniously by any evolutionary tree, and 𝑠 is equal to the actual number of state changes of a given character observed on a given tree. Possible values range from 0 to 1.0. CI values closer 111 to 1.0 indicate minimal homoplasy across an evolutionary tree according to parsimony, whereas CI values closer to 0 indicate high character state change across an evolutionary tree, and therefore more homoplasy. RI values for a given character across an evolutionary tree are calculated using Equation 2: 𝑅𝐼 = 𝑔−𝑠 𝑔−𝑚 Where 𝑔 is equal to the greatest amount of change that a character requires on any evolutionary tree, and 𝑚 and 𝑠 are as defined above. As with CI, possible RI values range from 0 to 1.0. RI values closer to 1.0 indicate no homoplasy, and all similarities in character states among branches and nodes of a tree are a result of homology (synapomorphy). RI values closer to 0 indicate that a given character shows as much homoplasy as possible, and that any similarities in character states among branches and nodes of a tree are acquired independently and do not result from homology (synapomorphy). The effects of missing and/or non-applicable character scorings on measuring phylogenetic signal. Initial results from the d-Statistic (Fig. S6-S9) revealed that higher median phylogenetic signal is present in characters corresponding to jaws and palate and axial regions of the squamate skeleton. However, further scrutiny revealed that d-Statistic values for each character have a strong inverse relationship with missing and/or non-applicable character scorings (Fig. S12, S13), and that characters corresponding to underrepresented regions had significantly higher median percentages of missing data (GEA: p= 0.00011; SEA: p= 5.377x10 -5 , Fig. S11). Missing data led to higher uncertainty in ancestral probability, which in turn led to lower ranges d- Statistic values (Supplementary dataset S47). As a result, it was not appropriate to include any character data from the GEA and SEA datasets with more than 0% missing data into these 112 analyses. However, characters from overrepresented and underrepresented regions of the squamate skeleton with 0% missing remained and were included in the analysis presented here. Additionally, the ancestral state calculations we used in the software BayesTraits to calculate the d-Statistic cannot calculate values for constant characters (e.g., characters that have the same score for all taxa included in the analysis). This resulted in close to two-thirds of the original amount of characters having to be removed from these analyses. Despite the removal of a large amount of phylogenetic data for the d-Statistic, we still retained enough data to observe meaningful patterns in phylogenetic signal among the anatomical regions in both limbed squamates (i.e., most lizards) and limbless squamates (i.e., snakes, amphisbaenians, dibamids, other limbless lizards). Because of the extreme disparities in bauplans among extant limbed lizards and limbless groups of squamates, it is unsurprising that there would be a large amount of missing/non-applicable characters, particularly those associated with the pectoral girdle, pelvic girdle, and appendicular elements. To minimize the limbed/limbless disparities in applicable characters, we ran the d- Statistic analyses for limbed taxa and limbless taxa for both the GEA and SEA datasets (Figure S14-S18, Supplementary Data S48-S57). We also removed five legged squamate taxa from the GEA dataset due to the fact that they were only scored for skull characters: Colobosaura modesta, Cordylosaurus subtesselatus, Xenosaurus platyceps, Leiosaurus catamarcensis, and Urostrophus vautieri (Supplementary Data S48). Because of the large quantity of snake taxa in the GEA dataset, we also ran an analysis of the d-Statistic using exclusively taxa contained within Serpentes (Supplementary Data S52, S57, Figure S19). 113 While more characters were excluded for the d-Statistic analyses than in the CI and RI analyses, the general patterns in phylogenetic signal were similar among all three analyses. Statistical analyses revealed no significant difference in retained phylogenetic signal among characters corresponding to overrepresented and underrepresented regions of the squamates skeleton in the fossil record. These results show that while we could only include characters for which every taxon could be scored in calculating the d-Statistic, the three measurements of phylogenetic signal, using different evolutionary frameworks and different hypotheses of squamate relationships (GEA, SEA), produced similar results. 114 Supplementary Figures Figure S1. Schematic diagram of an example squamate skeleton (modeled after Uta stansburiana, lower image), with colorized anatomical regions used in this study for sampling of fossil squamate collections, and example fossil squamate elements. A) Jaws and palatal elements (inset: DMNH EPV.119554 Scincomorpha partial left dentary, from Woolley, Smith & Sertich (2020) 3 . B) Posterior cranial elements (inset: YPM (unnumbered), partial frontal). C) Dermal elements (osteoderms) (inset: DMNH EPV.119455, Anguidae osteoderm, from Woolley, Smith & Sertich (2020) 3 . D) Axial elements (inset: UU MAA 7173, Ophisaurus partial trunk vertebra, from Georgalis et al. (2019 )4 . E) Pectoral girdle (inset: YPM 3230, Polyglyphanodon sternbergi scapulocoracoid) F) Appendicular elements (inset: YPM 3230, Polyglyphanodon sternbergi forelimb) G) Pelvic girdle (inset: YPM 3230, Polyglyphanodon sternbergi incomplete pelvis). 1 mm 1 mm 1 cm 1 mm 1 cm 1 cm 1 cm A B D G C F E 115 Figure S2. Workflow for keyword search-sampling Yale Peabody Museum’s electronic collections database. Yale Peabody Museum- Vertebrate Paleontology Collections online collections database search workflow 1. Go to: https://collections.peabody.yale.edu/search/ 2. Click on “Vertebrate Paleontology” 3. Type in “Squamata” in “Advanced Search” 4. Check “is Fossil” under “Limit To” 5. Click “Export Records”: “Export to CSV (Limit 500)”. Repeat exports for all specimens 116 Figure S3. Distribution skeletal elements sampled and sourced phylogenetic characters. A) Distributions of skeletal element occurrences. B) Distributions of phylogenetic characters per anatomical region of both datasets used in this study. Dermal 24.25% Jaws + Palate 36.49% Axial 15.61% Pelvic 0.72% In-person sampling Pectoral 0.60% Electronic Collections Databases Posterior Cranial 4.77% Jaws + Palate 37.56% Axial 48.72% Pectoral 0.99% Pelvic 1.27% Appendicular 4.19% Dermal 2.50% Total skeletal element occurrences Posterior Cranial 4.74% Jaws + Palate 37.49% Axial 46.79% Pectoral 0.96% Pelvic 1.24% Appendicular 5.02% Dermal 3.76% Posterior Cranial 4.32% Appendicular 18.01% A n = 14,417 (incl. 343 Squamata indet.) n = 833 n = 13,584 Morphological characters = 610 Morphological characters = 347 Simões et al. (2018) Posterior Cranial 34.29% Jaws + Palate 28.53% Axial 14.99% Pectoral 7.21% Pelvic 3.17% Appendicular 10.09% Dermal 0.58% Gauthier et al. (2012) Posterior Cranial 43.61% Jaws + Palate 28.03% Axial 4.10% Pectoral 4.92% Pelvic 2.95% Appendicular 7.05% Dermal 2.62% B Soft tissue/other 6.72% Soft tissue/other 1.15% 117 Figure S4. Distributions of CI and RI values per anatomical bin for the GEA dataset. A) Consistency Index distributions. B) Retention Index distributions. Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal Other Characters 0.0 0.2 0.4 0.6 0.8 1.0 Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal Other Characters 0.0 0.2 0.4 0.6 0.8 1.0 CI RI CI and RI distributions: Gauthier et al. (2012) A B n=165 n=165 n=246 n=246 n=22 n=22 n=30 n=30 n=17 n=17 n=36 n=36 n=15 n=15 n=41 n=41 118 Figure S5. Distributions of CI and RI values per anatomical bin for the SEA dataset. A) Consistency Index distributions. B) Retention Index distributions. CI and RI distributions: Simões et al. (2018) A B CI RI Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal 0.0 0.2 0.4 0.6 0.8 1.0 Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal 0.0 0.2 0.4 0.6 0.8 1.0 n=71 n=71 n=82 n=82 n=35 n=35 n=14 n=14 n=6 n=6 n=12 n=12 n=2 n=2 119 Figure S6. Summary of parsimony-based measurements of phylogenetic signal, with character matrices and topologies swapped. A) Distribution of CI values for GEA matrix vs. SEA topology characters corresponding to overrepresented skeletal elements in the squamate fossil record (See inset, center: overrepresented and underrepresented fossil skeletal regions mapped onto a schematic diagram of U. stansburiana) and all underrepresented skeletal elements in the squamate fossil record. B) Distribution of RI values for same GEA matrix vs. SEA topology character bins as in (A). C) Distribution of CI values of SEA matrix vs. GEA topology characters. D) Distribution of RI values of SEA matrix vs. GEA topology characters. Underrepresented fossil skeletal regions Overrepresented fossil skeletal regions Consistency Index Retention Index Overrepresented Underrepresented Gauthier et al. (2012) character matrix Overrepresented Underrepresented Overrepresented Underrepresented 0.0 0.2 0.4 0.6 0.8 1.0 A B C D 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 Simões et al. (2018) topology vs. Simões et al. (2018) character matrix Gauthier et al. (2012) topology vs. CI CI RI RI Consistency Index Retention Index Overrepresented Underrepresented 0.0 0.2 0.4 0.6 0.8 1.0 n = 143 n = 143 n = 281 n = 281 n = 101 n = 108 n = 101 n = 108 120 Figure S7. Distributions of CI and RI values per anatomical bin for the GEA matrix vs. SEA topology dataset. A) Consistency Index distributions. B) Retention Index distributions. CI RI CI and RI distributions: GEA Character Matrix vs. SEA Topology A B Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal Other Characters 0.0 0.2 0.4 0.6 0.8 1.0 Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal Other Characters 0.0 0.2 0.4 0.6 0.8 1.0 n=127 n=173 n=16 n=26 n=12 n=24 n=11 n=35 n=127 n=173 n=16 n=26 n=12 n=24 n=11 n=35 121 Figure S8. Distributions of CI and RI values per anatomical bin for the SEA matrix vs. GEA topology dataset. A) Consistency Index distributions. B) Retention Index distributions. CI and RI distributions: SEA Character Matrix vs. GEA Topology A B CI RI Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal 0.0 0.2 0.4 0.6 0.8 1.0 Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal 0.0 0.2 0.4 0.6 0.8 1.0 n=67 n=74 n=34 n=14 n=6 n=12 n=2 n=67 n=74 n=34 n=14 n=6 n=12 n=2 122 Figure S9. Sample visual representations of the calculations of node probabilities, using the SEA dataset in BayesTraits (Meade & Pagel, 2016). A) overrepresented and underrepresented fossil skeletal regions mapped onto a schematic diagram of Uta stansburiana. B) Ancestral state probabilities (node entropies) for example character corresponding to overrepresented fossil B A Underrepresented Overrepresented Simões et al. (2018) Char. 85 Parietals, parietal table, shape margins: ventrally directed w/ sagittal crest ventrally directed w/o sagittal crest laterally directed Simões et al. (2018) Char. 4 Premaxillae, dentition: present absent medially only entirely absent Trioceros jacksonii Uromastyx aegyptia Oplurus cyclurus Pristidactylus Hoplocercus spinosus Polychrus marmoratus Crotaphytus collaris Liolaemus Leiocephalus carinatus Stenocercus Iguana iguana Phrynosoma modestum Xenosaurus grandis Pseudopus apodus Elgaria multicarinata Heloderma suspectum Lanthanotus borneensis Varanus salvator Cylindrophis ruffus Xenopeltis unicolor Anilius scytale Teius teyou Petracola ventrimaculatus Timon lepidus Lacerta viridis Rhineura floridana Bipes biporus Blanus cinereus Plestiodon fasciatus Mabuya mabouya Cordylus niger Broadleysaurus major Xantusia vigilis Dibamus novaeguineae Dactylocnemis pacificus Gekko gecko Coleonyx variegatus Sphenodon punctatus Underrepresented skeletal regions Overrepresented skeletal regions 123 squamate skeletal elements (Premaxilla, green color palette) and underrepresented fossil squamate skeletal elements (Parietal, blue color palette). Figure S10. Summary of distributions of d-Statistic values for the GEA dataset using time- calibrated fossil tips and 1 million-year uniform branch lengths. Distribution of δ: Gauthier et al. (2012) Dated fossil tips with 1 m.y. uniform branch lengths AB C D Distribution of δ: U: 0 - 0.001 Distribution of δ: U: 0 - 0.1 Distribution of δ: U: 0 - 1.0 δ-values Frequency Frequency δ-values Frequency δ-values Frequency Distribution of δ: U: 0 - 0.01 δ-values Frequency δ-values δ-values Frequency δ-values Frequency δ-values Outliers Outliers Outliers Outliers Underrepresented n=402 Overrepresented n=191 Median Underrepresented n=402 Overrepresented n=191 Median Underrepresented n=402 Overrepresented n=191 Median Underrepresented n=402 Overrepresented n=191 Median 0.05 0.1 0.15 0.2 0.25 0.3 10 20 30 0.35 40 0 4.48 1.57 200 400 600 800 1000 0 0.05 0.15 0.25 0.35 3.66 1.29 50 60 40 30 20 10 0 Frequency 0.05 0.1 0.15 0.2 0.25 12345 6 0.3 0 0.1 0.2 10 20 30 40 50 60 70 0 0.3 0.05 0.1 0.15 123 0.2 04 0.05 0.1 0.15 10 20 30 40 50 60 0 0.2 0.1 0.2 0.3 510 15 0.4 20 0 0.15 0.25 0.35 0.05 1.50 0.83 0.77 0.54 124 Figure S11. Summary of distributions of d-Statistic values for the GEA dataset using time- calibrated fossil tips and 3 million-year uniform branch lengths. Distribution of δ: U: 0 - 0.001 Distribution of δ: Gauthier et al. (2012) Dated fossil tips with 3 m.y. uniform branch lengths AB C Distribution of δ: U: 0 - 0.1 D Distribution of δ: U: 0 - 1.0 200 400 600 800 1000 δ-values Frequency δ-values 0 0.05 0.1 0.15 10 20 30 0.2 40 0 0.05 0.1 0.15 0.2 Frequency 0.05 0.1 0.15 0.2 0.25 0 2468 10 δ-values Frequency 10 20 30 40 50 60 0 0.05 0.15 0.25 02 4 135 0.05 0.1 0.15 0.2 10 20 30 40 50 060 0.05 0.1 0.15 0.2 δ-values Frequency δ-values Frequency δ-values Frequency δ-values Frequency 4.27 1.54 Outliers Distribution of δ: U: 0 - 0.01 δ-values Frequency Underrepresented n=402 Overrepresented n=191 Median 0.05 0.1 0.15 0.2 0.25 510 15 0.3 0 0 20 3.15 1.09 0.1 0.2 0.3 10 20 30 40 50 Outliers 1.50 0.83 Outliers 0.92 0.53 Outliers Underrepresented n=402 Overrepresented n=191 Median Underrepresented n=402 Overrepresented n=191 Median Underrepresented n=402 Overrepresented n=191 Median 0 125 Figure S12. Summary of distributions of d-Statistic values for the GEA dataset using time- calibrated fossil tips and 5 million-year uniform branch lengths. Distribution of δ: Gauthier et al. (2012) Dated fossil tips with 5 m.y. uniform branch lengths AB CD Distribution of δ: U: 0 - 0.001 Distribution of δ: U: 0 - 0.1 Distribution of δ: U: 0 - 1.0 δ-values Frequency Frequency δ-values Frequency δ-values Frequency Underrepresented n=402 Overrepresented n=191 Median Distribution of δ: U: 0 - 0.01 δ-values Frequency Underrepresented n=402 Overrepresented n=191 Median Underrepresented n=402 Overrepresented n=191 Median Underrepresented n=402 Overrepresented n=191 Median δ-values δ-values Frequency δ-values Frequency δ-values Outliers Outliers Outliers Outliers 4.48 1.57 0.1 0.2 0.3 200 400 600 800 1000 0 0.4 0.05 0.1 0.15 10 20 30 40 50 60 0 0.2 Frequency 10 20 30 40 50 60 0 0.15 0.1 0.05 0.1 0.2 10 20 30 40 50 0 0.3 0.05 0.1 0.15 0.2 0.25 10 20 30 40 0 0.3 510 15 0.05 0.1 0.2 0.15 0.25 020 0.05 0.1 12 345 6 0 0.15 0.05 0.1 0.15 0.2 0.25 1234 5 0 0.3 2.99 1.06 1.38 0.81 1.05 0.55 126 Figure S13. Summary of distributions of d-Statistic values for the SEA dataset. AB CD Outliers 0.05 0.1 0.15 0.2 10 30 40 20 0 0.25 Underrepresented n=139 Overrepresented n=117 Median Distribution of δ: U: 0 - 0.001 Frequency δ-values 4.13 5 10 15 20 100 020 40 60 80 30 δ-values Frequency Frequency 0.05 0.1 12345 0.15 6 0 Distribution of δ: U: 0 - 0.01 2.10 1.27 δ-values Underrepresented n=139 Overrepresented n=117 Median Outliers 0.05 0.1 0.1 0.3 0.2 0.4 0.5 0 0.15 Underrepresented n=139 Overrepresented n=117 Median 0.0707 0.0694 Distribution of δ: U: 0 - 0.1 Frequency δ-values 0.05 0.1 0.15 0.2 01 2 3 4 5 6 δ-values Frequency Outliers 0.05 0.1 0.15 0.2 0.25 0.3 0.002 0.004 0.006 0.008 0.01 0 0.35 Underrepresented n=139 Overrepresented n=117 Median Distribution of δ: U: 0 - 1.0 0.00385 0.00394 Frequency δ-values 1.5 0.5 1.0 2.0 0.4 0.8 0 δ-values Frequency Distribution of δ: Simões et al. (2018) No Outliers 8.49 127 Figure S14. Correlation between % Missing/non-applicable character scorings (x-axis) and overrepresented/underrepresented fossil squamate skeletal regions. For both phylogenetic datasets, underrepresented fossil skeletal regions from the initial sampling have a higher frequency of missing/non-applicable character scorings. % Missing character data Frequency 0.1 0.2 0.3 0.4 0.5 20 40 60 80 0.6 0 % Missing character data Frequency 0.05 0.1 0.15 0.2 0.25 20 40 60 80 n=402 n=191 Median 0.3 100 0 Gauthier et al. (2012): Missing character data 100 Simões et al. (2018): Missing character data n=139 n=117 Median Underrepresented fossil skeletal regions Overrepresented fossil skeletal regions 128 Figure S15. XY scatterplot of the relationship between % Missing/non-applicable character scorings vs. d-statistic values of characters in the Gauthier et al. (2012) dataset. Data is separated into overrepresented (blue) and underrepresented (orange) anatomical regions in the squamate fossil record. 0 5 10 15 20 25 30 35 40 45 50 010 20 30 40 50 60 70 80 90 100 δ-values % Missing character data Gauthier et al. (2012): % Missing character data vs. δ-values Overrepresented Underrepresented R 2 = 0.7317 R 2 = 0.8447 y = 8.367e -0.049x y = 6.9134e -0.044x 129 Figure S16. XY scatterplot of the relationship between % Missing/non-applicable character scorings vs. d-statistic values of characters in the Simões et al. (2018) dataset. Data is separated into overrepresented (blue) and underrepresented (orange) anatomical regions in the squamate fossil record. 0 1 2 3 4 5 6 010 20 30 40 50 60 70 80 90 100 % Missing character data Simões et al. (2018): % Missing character data vs. δ - values Overrepresented Underrepresented R 2 = 0.3619 R 2 = 0.5357 y = 2.2073e -0.031x y = 2.20667e -0.033x δ-values 130 Figure S17. Summary of distributions of d-Statistic values for legged taxa from the GEA dataset using time-calibrated fossil tips, 78 calibrated internal nodes from Pyron (2017) and 3 million-year uniform branch lengths. Distribution of δ: U: 0 - 0.001 Distribution of δ: Gauthier et al. (2012) AB C Distribution of δ: U: 0 - 0.1 D Distribution of δ: U: 0 - 1.0 Legged taxa; dated fossil tips + dated internal nodes; 3 m.y. uniform branch lengths δ-values Frequency δ-values Frequency δ-values Frequency δ-values Frequency δ-values Frequency δ-values Frequency δ-values Frequency 50 0 0.02 100 150 0.06 0.10 20 40 60 75 0 0.05 0.10 0.15 10 20 30 40 0 0.02 0.04 0.06 10 20 15 5 0 0.02 0.04 0.06 0.05 0.03 0.01 510 15 20 25 30 0 0.05 0.10 0.15 0.20 10 02 4 6 8 0.05 0.10 0.15 0.20 510 15 20 25 30 0 0.20 0.40 0.60 10 02 4 6 8 0.1 0.2 0.3 0.4 0.5 0.6 6.73 6.60 Outliers Distribution of δ: U: 0 - 0.01 δ-values Frequency Outliers Outliers Outliers Underrepresented n=121 Overrepresented n=74 Median 20.8 21.7 Underrepresented n=121 Overrepresented n=74 Median Underrepresented n=121 Overrepresented n=74 Median 1.28 1.44 Underrepresented n=121 Overrepresented n=74 Median 0.24 0.10 131 Figure S18. Summary of distributions of d-Statistic values for legged taxa from the GEA dataset using time-calibrated fossil tips, 78 calibrated internal nodes from Pyron (2017) and 5 million-year uniform branch lengths. Distribution of δ: Gauthier et al. (2012) Legged taxa; dated fossil tips + dated internal nodes; 5 m.y. uniform branch lengths AB CD Distribution of δ: U: 0 - 0.001 Distribution of δ: U: 0 - 0.1 Distribution of δ: U: 0 - 1.0 δ-values Frequency Frequency δ-values Frequency δ-values Frequency Distribution of δ: U: 0 - 0.01 δ-values Frequency δ-values δ-values Frequency δ-values Frequency δ-values Outliers Outliers Outliers Frequency 0.02 0.06 0.10 510 15 20 25 30 35 0 0.02 0.06 50 100 0.10 0 150 0.02 0.04 0.06 0.08 60 40 20 0 0.10 75 510 15 20 25 30 0 0.05 0.10 0.15 0.20 0.05 0.1 0.15 24 6 8 0.2 0 10 2 4 6 8 0 10 0.1 0.2 0.3 0.4 0.5 0.6 0.7 Outliers 0.02 0.04 0.06 0.08 510 0.10 015 510 15 20 25 0 30 0.1 0.3 0.5 0.7 Underrepresented n=121 Overrepresented n=74 Median 6.29 6.20 Underrepresented n=121 Overrepresented n=74 Median 20.8 21.2 Underrepresented n=121 Overrepresented n=74 Median 1.09 1.40 Underrepresented n=121 Overrepresented n=74 Median 0.24 0.06 132 Figure S19. Summary of distributions of d-Statistic values for legged taxa from the GEA dataset using time-calibrated fossil tips, 78 calibrated internal nodes from Pyron (2017) and 7 million-year uniform branch lengths. Distribution of δ: Gauthier et al. (2012) Legged taxa; dated fossil tips + dated internal nodes; 7 m.y. uniform branch lengths AB C D Distribution of δ: U: 0 - 0.001 Distribution of δ: U: 0 - 0.1 Distribution of δ: U: 0 - 1.0 δ-values Frequency Frequency δ-values Frequency δ-values Frequency Distribution of δ: U: 0 - 0.01 δ-values Frequency δ-values δ-values Frequency δ-values Frequency δ-values Outliers Outliers Outliers Underrepresented n=121 Overrepresented n=74 Median 0.05 0.1 510 0.15 015 Outliers Underrepresented n=121 Overrepresented n=74 Median 0.05 0.1 510 15 20 25 0.15 030 0.05 0.1 0.15 246 8 0.2 0 10 Underrepresented n=121 Overrepresented n=74 Median 0.1 0.2 0.3 0.4 0.5 2468 0.6 010 Underrepresented n=121 Overrepresented n=74 Median Frequency 50 100 0.02 0.06 0.10 0 150 0.02 0.04 0.06 0.08 10 20 30 40 50 60 0 0.10 0.05 0.1 0.15 0.2 510 15 20 25 30 0 0.25 510 15 20 25 0 0.2 0.4 0.6 30 20.31 20.08 5.53 5.41 1.48 0.95 0.24 0.04 133 Figure S20. Summary of distributions of d-Statistic values for the SEA dataset, using only legged taxa. AB CD Distribution of δ: U: 0 - 0.001 Frequency δ-values δ-values Frequency Distribution of δ: U: 0 - 0.01 δ-values Outliers Distribution of δ: U: 0 - 0.1 Frequency δ-values δ-values Frequency Outliers Distribution of δ: U: 0 - 1.0 Frequency δ-values δ-values Frequency Distribution of δ: Simões et al. (2018) Legged Taxa No Outliers n=68 n=58 Median 0.05 0.1 12 3 4 5 0.15 6 0 2.37 2.22 0.05 0.10 10 20 30 40 50 60 0 0.15 510 15 020 0.05 0.1 0.15 n=68 n=58 Median 0.10 0.20 123 0.30 0 4 0.05 0.10 0.15 0.20 0.25 0.05 0.10 0.15 0.20 0 0.05 0.10 0.15 0.20 0 0.10 0.20 0.30 0.05 0.10 0.15 0.20 0 0.25 0.30 0.001 0.002 0.003 0.004 0.005 0.006 0.007 Outliers n=68 n=58 Median 0.062 0.067 7.39 8.14 n=68 n=58 Median 0.00502 0.00501 134 Figure S21. Distributions of d-Statistic for the pruned GEA character dataset using only taxa belonging to Serpentes (prior on transition rates for ancestral node probability calculations = 0.01). Inset: overrepresented and underrepresented fossil skeletal regions mapped onto a schematic diagram of Crotalus atrox. Histogram shows the distribution of d-values between GEA characters (time-calibrated fossil tips +78 calibrated internal nodes with minimum branch lengths of 5 million years) corresponding to overrepresented (green) and underrepresented (blue) fossil squamate skeletal elements. Frequency δ-values Underrepresented fossil skeletal regions Overrepresented fossil skeletal regions Distribution of δ: Gauthier et al. (2012) Serpentes Characters with 0% missing data n=39 n=34 Median 0.05 0.1 0.15 5 15 10 20 0 6.29 6.36 135 Figure S22. Summary of distributions of d-Statistic values for characters with 0% missing data in the GEA dataset using only limbed squamate taxa, time-calibrated fossil tips + 78 calibrated internal nodes, 5 million-year uniform branch lengths and prior character transition rate of 0.01. Distribution of δ-values (Prior transition rate = 0.01): Gauthier et al. (2012) Limbed squamates δ-values n=67 n=75 n=7 n=8 n=7 n=19 n=6 n=6 Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal Other Characters 010 20 30 40 136 Figure S23. Summary of distributions of d-Statistic values for characters with 0% missing data in the SEA dataset, using only limbed squamate taxa and a prior character transition rate of 0.01. Distribution of δ-values (Prior transition rate = 0.01): Simões et al. (2018) Limbed squamates Dermal δ-values Tooth-bearing Axial Cranial Pectoral Pelvic Appendicular 01 2 3 4 5 6 n=44 n=44 n=14 n=8 n=4 n=10 n=2 137 Figure S24. Summary of distributions of d-Statistic values for characters with 0% missing data in the GEA dataset using only limbless squamate taxa, time-calibrated fossil tips +78 calibrated internal nodes, 5 million-year uniform branch lengths and prior character transition rate of 0.01. Distribution of δ-values (Prior transition rate = 0.01): Gauthier et al. (2012) Legless squamates δ-values n=32 n=7 n=48 n=1 Jaws + Palate Posterior Cranial Dermal Other Characters 010 20 30 40 138 Figure S25. Summary of distributions of d-Statistic values for characters with 0% missing data in the GEA dataset using only taxa included in Serpentes (snakes), time-calibrated fossil tips +78 calibrated internal nodes, 5 million-year uniform branch lengths and prior character transition rate of 0.01. Distribution of δ-values (Prior transition rate = 0.01): Gauthier et al. (2012) Snakes δ-values n=31 n=1 n=37 n=1 n=3 Jaws + Palate Axial Posterior Cranial Dermal Other Characters 05 10 15 20 139 Figure S26. Summary of d-Statistic values for characters with 0% missing data, using swapped character matrices and topologies. A) GEA Matrix vs SEA Topology. B) SEA Matrix vs. GEA Topology. 0 0.05 0.1 0.15 12345 0.2 Distribution of δ: Simões et al. (2018) matrix vs. Gauthier et al. (2012) topology Frequency δ-values 6 Underrepresented fossil skeletal regions Overrepresented fossil skeletal regions Distribution of δ: Gauthier et al. (2012) matrix vs. Simões et al. (2018) topology n=111 n=73 Median Frequency δ-values n=67 n=57 Median 0.05 0.1 12345 0.15 0 AB 1.91 1.64 1.54 1.54 140 Figure S27. Summary of distributions of d-Statistic values for characters with 0% missing data in the GEA matrix vs. SEA topology dataset, using only limbed squamate taxa and a prior character transition rate of 0.01. Distribution of δ-values (Prior transition rate = 0.01): GEA Matrix vs. SEA Topology Limbed squamates δ-values n=66 n=68 n=7 n=8 n=7 n=17 n=5 n=6 Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal Other Characters 02468 141 Figure S28. Summary of distributions of d-Statistic values for characters with 0% missing data in the SEA matrix vs. GEA topology dataset, using only limbed squamate taxa and a prior character transition rate of 0.01. Distribution of δ-values (Prior transition rate = 0.01): SEA Matrix vs. GEA Topology Limbed squamates δ-values n=44 n=43 n=13 n=8 n=4 n=10 n=2 Jaws + Palate Axial Posterior Cranial Pectoral Pelvic Appendicular Dermal 0 123456 142 All supplementary data associated with this manuscript can be found at Dryad Digital Repository: https://doi.org/10.5061/dryad.m63xsj43b Dataset S1 (separate file). Source dataframe for fossil squamate electronic collections database from the Institute for Vertebrate Paleontology & Paleoanthropology (IVPP), Beijing, China. Dataset S2 (separate file). Source dataframe for fossil squamate electronic collections database from the Natural History Museum of Los Angeles County (LACM), Los Angeles, California, USA. Dataset S3 (separate file). Source dataframe for fossil squamate electronic collections database from the Natural History Museum London (NHMUK), London, UK. Dataset S4 (separate file). Source dataframe for fossil squamate electronic collections database from the University of Florida Museum of Natural History, Gainesville, Florida, USA. Dataset S5 (separate file). Source dataframe for fossil squamate electronic collections database from the Smithsonian National Museum of Natural History (USNM), Washington, D.C., USA. Dataset S6 (separate file). Source dataframe for fossil squamate electronic collections database from the Yale Peabody Museum of Natural History (YPM), New Haven, Connecticut, USA. Dataset S7 (separate file). Combined dataframe of all specimen information from sampled fossil squamate digital collections Dataset S8 (separate file). Dataframe of all skeletal element occurrences assigned to mosasaurs in surveyed digital collections. Dataset S9 (separate file). Dataframe of all skeletal element occurrences assigned to lizards in surveyed digital collections. 143 Dataset S10 (separate file). Dataframe of all skeletal element occurrences assigned to snakes in surveyed digital collections. Dataset S11 (separate file). Dataframe of all skeletal element occurrences assigned to “Squamata indet.” in surveyed digital collections. Dataset S12 (separate file). Dataframe of all specimen info for squamates surveyed in-person. Dataset S13 (separate file). Dataframe of all fossil squamate skeletal element occurrences in in- person collections surveys Dataset S14 (separate file). Dataframe summarizing all fossil squamate skeletal element occurrences in surveyed collections. Dataset S15 (separate file). .tre file of the Strict Consensus Gauthier et al. (2012) topology used for calculating CI and RI in this study, with fossil taxa dropped. Dataset S16 (separate file). .tre file of the Strict Consensus Simões et al. (2018) topology used for calculating CI and RI in this study, with fossil taxa dropped. Dataset S17 (separate file). NEXUS file of the Gauthier et al. (2012) topology used for calculating CI and RI in this study, with fossil taxa dropped. Dataset S18 (separate file). NEXUS file of the Simões et al. (2018) topology used for calculating CI and RI in this study, with fossil taxa dropped. Dataset S19 (separate file). Dataframe of the average character CI values for the Gauthier et al. (2012) dataset. 144 Dataset S20 (separate file). Dataframe of the average character CI values for the Simões et al. (2018) dataset. Dataset S21 (separate file). Dataframe of the average character RI values for the Gauthier et al. (2012) dataset. Dataset S22 (separate file). Dataframe of the average character RI values for the Simões et al. (2018) dataset. Dataset S23 (separate file). Results of the statistical tests comparing CI and RI value distributions per surveyed anatomical bin in squamate collections. Dataset S24 (separate file). NEXUS file of the Bayesian consensus tree from Simões et al. (2018) dataset, used in the calculation of the d-Statistic. Dataset S25 (separate file). NEXUS file of the strict consensus tree from the Gauthier et al. (2012) dataset (dated fossil tips with 3 million-year uniform branch lengths), used in the calculation of the d-Statistic. Dataset S26 (separate file). NEXUS file of the strict consensus tree from the Gauthier et al. (2012) dataset (dated fossil tips with 1 million -year uniform branch lengths), used in the calculation of the d-Statistic. Dataset S27 (separate file). NEXUS file of the strict consensus tree from the Gauthier et al. (2012) dataset (dated fossil tips with 5 million -year uniform branch lengths), used in the calculation of the d-Statistic. 145 Dataset S28 (separate file). Dataframe of the Gauthier et al. (2012) character matrix, with constant characters removed, used for calculation of the d-Statistic. Dataset S29 (separate file). Dataframe of the Simões et al. (2018) character matrix, with constant characters removed, used for calculation of the d-Statistic. Dataset S30 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 1 million-year uniform branch lengths, U: 0-0.001). Dataset S31 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 1 million-year uniform branch lengths, U: 0-0.01). Dataset S32 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 1 million-year uniform branch lengths, U: 0-0.1). Dataset S33 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 1 million-year uniform branch lengths, U: 0-1.0). Dataset S34 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 3 million-year uniform branch lengths, U: 0-0.001). Dataset S35 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 3 million-year uniform branch lengths, U: 0-0.01). Dataset S36 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 3 million-year uniform branch lengths, U: 0-0.1). 146 Dataset S37 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 3 million-year uniform branch lengths, U: 0-1.0). Dataset S38 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 5 million-year uniform branch lengths, U: 0-0.001). Dataset S39 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 5 million-year uniform branch lengths, U: 0-0.01). Dataset S40 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 5 million-year uniform branch lengths, U: 0-0.1). Dataset S41 (separate file). Dataframe of d-Statistic values from the Gauthier et al. (2012) dataset (dated fossil tips with 5 million-year uniform branch lengths, U: 0-1.0). Dataset S42 (separate file). Dataframe of d-Statistic values from Simões et al. (2018) dataset (U: 0-0.001). Dataset S43 (separate file). Dataframe of d-Statistic values from Simões et al. (2018) dataset (U: 0-0.01). Dataset S44 (separate file). Dataframe of d-Statistic values from Simões et al. (2018) dataset (U: 0-0.1). Dataset S45 (separate file). Dataframe of d-Statistic values from Simões et al. (2018) dataset (U: 0-1.0). 147 Dataset S46 (separate file). Results of bootstrap tests of d-Statistic distributions for surveyed anatomical bins for both the Gauthier et al. (2012) and Simões et al. (2018) datasets. Dataset S47 (separate file). Data and charts assessing and testing the relationships between the percentage of missing/non-applicable characters and measurements of phylogenetic signal. Dataset S48 (separate file). Dataframe of the Gauthier et al. (2012) character matrix, with constant characters and characters with missing/non-applicable scores removed and using only limbed squamate taxa, used for calculation of the d-Statistic. Dataset S49 (separate file). Dataframe of the Simões et al. (2018) character matrix, with constant characters and characters with missing/non-applicable scores removed and using only limbed squamate taxa, used for calculation of the d-Statistic. Dataset S50 (separate file). Dataframe of the Gauthier et al. (2012) character matrix, with constant characters and characters with missing/non-applicable scores removed and using only limbless squamate taxa, used for calculation of the d-Statistic. Dataset S51 (separate file). Dataframe of the Gauthier et al. (2012) character matrix, with constant characters and characters with missing/non-applicable scores removed and using only snake taxa, used for calculation of the d-Statistic. Dataset S52 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 3 million-year uniform branch lengths, U: 0-0.001). 148 Dataset S53 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 3 million-year uniform branch lengths, U: 0-0.01). Dataset S54 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 3 million-year uniform branch lengths, U: 0-0.1). Dataset S55 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 3 million-year uniform branch lengths, U: 0-1.0). Dataset S56 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 5 million-year uniform branch lengths, U: 0-0.001). Dataset S57 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 5 million-year uniform branch lengths, U: 0-0.01). Dataset S58 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 5 million-year uniform branch lengths, U: 0-0.1). 149 Dataset S59 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 5 million-year uniform branch lengths, U: 0-1.0). Dataset S60 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 7 million-year uniform branch lengths, U: 0-0.001). Dataset S61 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 7 million-year uniform branch lengths, U: 0-0.01). Dataset S62 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 7 million-year uniform branch lengths, U: 0-0.1). Dataset S63 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 7 million-year uniform branch lengths, U: 0-1.0). Dataset S64 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa from Simões et al. (2018) dataset (U: 0-0.001). Dataset S65 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa from Simões et al. (2018) dataset (U: 0-0.01). 150 Dataset S66 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa from Simões et al. (2018) dataset (U: 0-0.1). Dataset S67 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbed squamate taxa from Simões et al. (2018) dataset (U: 0-1.0). Dataset S68 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only limbless squamate taxa in the Gauthier et al. (2012) dataset (dated fossil tips and 78 calibrated internal nodes with 5 million-year uniform branch lengths, U: 0-0.01). Dataset S69 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only squamate taxa belonging to Serpentes in the Gauthier et al. (2012) dataset (dated 151 fossil tips and 78 calibrated internal nodes with 5 million-year uniform branch lengths, U: 0- 0.01). Dataset S70 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only legged squamate taxa in the Gauthier et al. (2012) character matrix mapped onto the Simões et al. (2018) 6 topology. Dataset S71 (separate file). Dataframe of d-Statistic values for characters with 0% missing data, using only legged squamate taxa in the Simões et al. (2018) character matrix mapped onto the Gauthier et al. (2012) topology. Dataset S72 (separate file). Dataframe of character CI values for characters with 0% missing data, using only legged squamate taxa in the Gauthier et al. (2012) character matrix mapped onto the Simões et al. (2018) topology. Dataset S73 (separate file). Dataframe of character CI values for characters with 0% missing data, using only legged squamate taxa in the Simões et al. (2018) character matrix mapped onto the Gauthier et al. (2012) topology. Dataset S74 (separate file). Dataframe of character RI values for characters with 0% missing data, using only legged squamate taxa in the Gauthier et al. (2012) character matrix mapped onto the Simões et al. (2018) topology. Dataset S75 (separate file). Dataframe of character RI values for characters with 0% missing data, using only legged squamate taxa in the Simões et al. (2018) character matrix mapped onto the Gauthier et al. (2012) topology. 152 Dataset S76 (separate file). NEXUS file of the Simões et al. (2018) character matrix, containing only overlapping extant taxa with the Gauthier et al. (2012) dataset, used for calculating CI and RI in this study. Dataset S77 (separate file). NEXUS file of the Gauthier et al. (2012) character matrix, containing only overlapping extant taxa with the Simões et al. (2018) dataset, used for calculating CI and RI in this study. Dataset S78 (separate file). Dataframe of the Gauthier et al. (2012) character matrix, with constant characters and characters with missing/non-applicable scores removed and using only limbed squamate taxa overlapping with the Simões et al. (2018) character matrix, used for calculation of the d-Statistic. Dataset S79 (separate file). Dataframe of the Simões et al. (2018) character matrix, with constant characters and characters with missing/non-applicable scores removed and using only 153 limbed squamate taxa overlapping with the Gauthier et al. (2012) character matrix, used for calculation of the d-Statistic. Dataset S80 (separate file). NEXUS file of the Gauthier et al. (2012) 5 tree, using only limbed squamate taxa overlapping with the Simões et al. (2018) 6 tree used for calculation of the d- Statistic. Dataset S81 (separate file). NEXUS file of the Simões et al. (2018) tree, using only limbed squamate taxa overlapping with the Gauthier et al. (2012) tree, used for calculation of the d- Statistic. Dataset S82 (separate file). NEXUS file of the strict consensus tree from the Gauthier et al. (2012) dataset (dated fossil tips with 3 million-year uniform branch lengths with 78 dated internal nodes from Pyron, 2017), used in the calculation of the d-Statistic. Dataset S83 (separate file). NEXUS file of the strict consensus tree from the Gauthier et al. (2012) dataset (dated fossil tips with 5 million -year uniform branch lengths with 78 dated internal nodes from Pyron, 2017), used in the calculation of the d-Statistic. Dataset S84 (separate file). NEXUS file of the strict consensus tree from the Gauthier et al. (2012) dataset (dated fossil tips with 7 million -year uniform branch lengths with 78 dated internal nodes from Pyron, 2017), used in the calculation of the d-Statistic. 4S Literature Cited 1. Kluge, A. G., and J. S. Farris. 1969. Quantitative phyletics and the evolution of anurans. Systematic Biology 18(1):1-32. 154 2. Farris, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5(4):417- 419. 3. Woolley, C. H., N. D. Smith, and J. J. Sertich. 2020. New fossil lizard specimens from a poorly- known squamate assemblage in the Upper Cretaceous (Campanian) San Juan Basin, New Mexico, USA. PeerJ 8:e8846. 4. Georgalis, G., A. Villa, I. Martin, D. Vasilyan, and M. Delfino. 2019. Fossil amphibians and reptiles from the Neogene locality of Maramena (Greece), the most diverse European herpetofauna at the Miocene/Pliocene transition boundary. 5. Gauthier, J. A., M. Kearney, J. A. Maisano, O. Rieppel, and A. D. B. Behlke. 2012. Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record. Bulletin of the Peabody Museum of Natural History 53(1):3-308, 306. 6. Simões, T. R., M. W. Caldwell, M. Tałanda, M. Bernardi, A. Palci, O. Vernygora, F. Bernardini, L. Mancini, and R. L. Nydam. 2018. The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps. Nature 557(7707):706-709. 7. Meade, A., and M. Pagel. 2016. BayesTraits V3.01. Available at http://www.evolution.rdg.ac.uk/BayesTraitsV3.0.1/BayesTraitsV3.0.1.html. 8. Borges, R., J. P. Machado, C. Gomes, A. P. Rocha, and A. Antunes. 2019. Measuring phylogenetic signal between categorical traits and phylogenies. Bioinformatics 35(11):1862- 1869. 9. Pyron, R. A. 2017. Novel approaches for phylogenetic inference from morphological data and total-evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians). Systematic Biology 66(1):38-56. 155 CHAPTER 5: UNIQUE COUPLING OF FOSSIL LIZARD DIVERSITY AND SKELETAL COMPLETENESS IN THE LATE CRETACEOUS GOBI DESERT OFFERS A PHYLOGENETIC LENS ON LAGERSTÄTTEN This paper is in review as: Woolley, C. H., D. J. Bottjer, F.A. Corsetti, and N. D. Smith. (In Review). Unique coupling of fossil lizard diversity and skeletal completeness in the Late Cretaceous Gobi Desert offers a phylogenetic lens on lagerstätten. Proceedings of the National Academy of Science. Abstract Exceptionally preserved fossil deposits hold an outsized influence over our understanding of biodiversity and evolution in the rock record, but this so-called “lagerstätten effect” remains challenging to classify and measure. Here, I quantify the “lagerstätten effect” on the amount of phylogenetic information available in the global fossil records of 1,327 species of non-avian theropod dinosaurs, Mesozoic birds, and fossil squamates (e.g., lizards, snakes, mosasaurs). During this comparative survey, I unexpectedly find that aeolian deposits of the Late Cretaceous Gobi Desert of Mongolia and China preserve exceptionally complete squamate anatomical and phylogenetic data, such that they exert an anomalously large influence on fossil record completeness on global scales and the deep-time structure of squamate evolutionary relationships. These results offer a novel lens through which to examine the effects of lagerstätten on biological patterns through time and space, and invites further assessments quantifying the availability of evolutionary information in the rock record. 156 5.1. Introduction While the fossil record is rich, the majority of available palaeobiological data resides in partial, disarticulated, and incomplete specimens. However, unusually rare confluences of deposition, taphonomy, and diagenesis can produce exceptionally preserved fossil assemblages that reveal exquisitely detailed information about ancient life and the ecosystems in which they lived. The resulting fossil deposits, known as “lagerstätten”, have been divided into two types, Konservat-lagerstätten and Konzentrat-lagerstätten (Seilacher, 1970 ). Konservat-lagerstätten (Seilacher, 1970 , Allison, 1988) are characterized by the preservation of difficult to fossilize features (e.g., soft tissues) and often form under quick burial and anoxia/hypoxia associated with stagnation deposits, obrution deposits, and conservation traps such as peat or amber (Seilacher et al., 1985 ). Konzentrat-lagerstätten (Seilacher, 1970 ), on the other hand, are characterized by the sheer number of fossilized specimens found in a single deposit, and form under a different set of sedimentological conditions that favor dense accumulation of fossilized remains (e.g., condensation deposits, placer deposits, and concentration traps; Seilacher et al. 1985 ). In the past half-century, spectacular fossil deposits from all over the world have been placed into these broad Konservat-vs.-Konzentrat-lagerstätten categories, revealing a spectrum of modes and settings in which exceptional preservation can occur (Seilacher et al., 1985; Bottjer et al., 2002). Konservat-and-Konzentrat-lagerstätten reveal information about aspects of ancient ecosystems that have a substantial impact on our understanding of fossil life compared to the typical fossil deposit. Lagerstätten are found across billions of years of geologic time (Bottjer et al., 2002), and include some of the most widely-known and well-understood deposits on the planet. Examples include the astonishing animal morphological disparity and presence of most modern animal phyla in the Middle Cambrian Burgess Shale in Canada (Briggs et al., 1994; 157 Hagadorn, 2002) that established the baseline for our understanding of early animal diversification. Another famous example includes the extraordinary, centuries-long influence of the roughly 250 fish species found in the Eocene Monte Bolca ichthyofauna in Italy on our understanding of fish paleobiology in deep time (Gaudant, 1997; Tang, 2002). Other examples are not necessarily restricted to such deep time, and can include more geologically-recent deposits such as the Pleistocene Rancho La Brea asphaltum deposits in California (Stock, 1930; DeSantis et al. 2019), which preserves a diverse faunal and floral assemblage containing mostly disarticulated skeletons, unique environmental preservation and ample evidence of inter-and- intraspecific interaction. The biological information we gain from rare lagerstätten deposits often substantially exceeds what is preserved in the vast majority of “normal” fossil deposits, and as such have been identified as having an anomalous impact on studies of ecology, diversification and extinction through time (Sepkoski, 1996). This impact, commonly referred to as the “lagerstätten effect”, can be at once a paleobiological boon to researchers (Bottjer et al., 2002) and a major source of bias in our understanding of the morphological evolution of a given group or groups of organisms (Sepkoski, 1996). The “lagerstätten effect” is famously acute in reconstructing global biodiversity changes through geologic time (Sepkoski, 1996). Lagerstätten often preserve such anomalously high amounts of fossil species relative to typical “baseline” sedimentary processes that estimations of global fossil diversity and abundance are more accurate when removing them from the dataset (Sepkoski, 1996). This paradoxical bias has other important downstream impacts in analytical paleobiology. In particular, when it comes to inferring the phylogenetic relationships of organismal groups using their fossil record, the “lagerstätten effect” on phylogenetic information content and incorporation of taxa into analyses remains underexplored, 158 and needs to be characterized to avoid bias in evolutionary interpretations (Smith, 1994 ; Sepkoski, 1996 ; Kidwell & Holland, 2002 ). Here, I use a quantitative approach to characterize the amount of phylogenetic information available in the formation-specific fossil records of three prominent tetrapod groups: non-avian theropod dinosaurs, birds, and squamates (e.g., lizards, snakes, amphisbaenians, and mosasaurs). I compare the fossil records of these three groups recovered from a well-known lacustrine konservat-lagerstätte (Barremian/Aptian Yixian and Jiufotang formations, the “Jehol Biota”, China), as well as the aeolian dune deposits of the Late Campanian Djadokhta/Baruungoyot formations in Mongolia and China. I suggest that deposits like the Djadokhta and Baruungoyot formations, although lacking traditional Konservat-and-Konzentrat- lagerstätten features (soft-bodied preservation, extreme abundance, etc.), still preserve a disproportionately high amount of phylogenetic information, such that they have an outsized, “lagerstätten effect” on our understanding of a group’s evolutionary history. Specifically, I highlight an unexpected finding: the preservation of skeletal anatomy and species diversity of lizards in the Upper Cretaceous aeolian deposits of the Gobi Desert (Sulimski, 1975 ; Borsuk-Bialynicka & Moody, 1984 ; Borsuk-Bialynicka & Alifanov, 1991 ; Dashzeveg et al., 1995 ; Dashzeveg et al., 2005 ; Gao & Norell, 2000 ) has an anomalously large influence on global-scale patterns of the availability of phylogenetic information in the fossil record of squamates, even when compared to diverse squamate assemblages found in established lagerstätten deposits. The pattern observed in squamates compares favorably to the well- established “lagerstätten effect” of the spectacular assemblage of birds from the Jehol Biota on our understanding of Mesozoic bird evolution (Brocklehurst et al., 2012; Chiappe & Qingjin, 2016). These results offer a novel lens through which to examine the effects of exceptional 159 preservation on phylogenetic information content in fossil groups, and invite further assessments quantifying the availability of evolutionary information in the rock record. 5.2. Results 5.2.1. General phylogenetic completeness of non-avian theropods, birds, and squamates In this quantitative approach to assessing the availability of phylogenetic information in the fossil record, I use the Character Completeness Metric 2 ( CCM2, Mannion & Upchurch, 2010; see Materials & Methods), which measures the percentage of phylogenetic characters that can be scored for all specimens assigned to a fossil species. The phylogenetic datasets corresponding to each group in this study (Fig. 1) contain hundreds of characters (non-avian theropods: 774, O’Connor et al., 2020; Mesozoic birds: 653, Brocklehurst et al., 2012; squamates: 860, this study) that reflect the variation in skeletal anatomy found therein. Non- avian theropods (Fig. 1A) and Mesozoic birds (Fig. 1B) have concentrations of phylogenetic characters that are more or less evenly distributed throughout the skeleton, whereas squamates (Fig. 1C) have over two-thirds of their phylogenetic characters concentrated in the skull and mandibles. This can probably be explained by the large amount of variation in the skulls of squamates and/or the presence of numerous legless lineages of squamates (e.g., snakes, amphisbaenians, dibamids), necessitating an emphasis on shared characters in the skull to assess higher level evolutionary relationships (Fig. S1;Gauthier et al., 2012; Simões et al., 2018). The generalized distributions of preserved phylogenetic information in non-avian theropods, Mesozoic birds, and squamates across time and space (Fig. 1D) reveal some noteworthy patterns. The squamate dataset contains the most species (n = 797) and spans the most geologic time (Middle Triassic to Late Pleistocene), yet on the whole preserves the least amount of phylogenetic information. Mesozoic birds contain the least amount of species (n = 160 128) and shortest span of geologic time (Late Jurassic – Late Cretaceous), have a median CCM2 value that is not statistically significantly different from that of squamates (α = 0.05, p = 0.07535, Supplemental Material), but have a relatively higher proportion of species that preserve a high amount of phylogenetic information. Non-avian theropods, as one of the most intensely-studied groups of fossil animals (Benton, 2008; 2010; Cashmore & Butler 2019) are both well-sampled (n = 402) and preserve a significantly higher median CCM2 value and distribution of CCM2 scores than Mesozoic birds and squamates (all p-values<<<< 0.05, Supplemental Material). 5.2.2. Preservation of phylogenetic information in the Early Cretaceous Jehol Biota Non-avian theropods and birds are famously well-preserved and well-represented in the Jehol Biota assemblages in the Barremian-Aptian Yixian and Jiufotang formations in the Liaoning and Inner Mongolia provinces of China (Fig. 2A; Zhou, 2014; Chiappe & Qingjin, 2016). Squamates, while not as abundant as theropods (including birds), still preserve remarkably complete specimens (Fig. 2A; Evans & Wang, 2005; Dong, Wang & Evans, 2017) that reveal intriguing aspects of squamate anatomical evolution (Dong, Wang & Evans, 2017) and biotic interactions (O’Connor et al., 2019). Side-by-side statistical comparisons of CCM2 distributions (Fig. 2A, Supplemental Material) of all three groups reflect a similar pattern to that observed in comparisons of their global distributions through time (Fig. 1D). Non-avian theropods preserve a significantly higher median CCM2 value (87.28%) and distributions of CCM2 values than those observed in both birds and squamates (all p-values < 0.05, Supplemental Material), and while birds preserve a higher median CCM2 value (75.57%) than squamates (55.17%) and more phylogenetic information overall, there is not a statistically 161 significant difference between their distributions (α = 0.05; Mann-Whitney U: p = 0.09584; Kolmogorov-Smirnov: p = 0.17650, Supplemental Material). 5.2.3. Preservation of phylogenetic information in the Late Cretaceous (Campanian) Gobi Desert The aeolian deposits of the late Campanian Djadokhta and Baruungoyot formations in Mongolia and China preserve one of the most iconic assemblages of theropod dinosaurs in the fossil record, including Velociraptor and myriad oviraptorosaurs and ornithomimosaurs (Norell & Makovicky, 1999; Currie 2000; Chinzorig et al., 2017). Additionally, the Campanian Gobi Desert preserves historically important bird fossils (Elzanowski, 1974, Chiappe et al., 2001; Varricchio et al., 2015), even though they are not as abundant as theropods. Where the truly remarkable preservation lies is within the record of squamates, with at least 50 described species of three-dimensionally-preserved skulls and partial skeletons (Sulimski, 1975 ; Borsuk- Bialynicka & Moody, 1984 ; Borsuk-Bialynicka & Alifanov, 1991 ; Gao & Norell, 2000). Side- by-side comparisons of the distributions of CCM2 values (Fig. 2B) among all three tetrapod groups show similar, high levels of preservation compared to the overall fossil records (Fig. 1D), similar to the patterns observed in the Jehol Biota (Fig. 2A). Unlike the Jehol Biota, however, there are no statistically significant differences in the median CCM2 percentages and distribution shapes in all three surveyed Campanian Gobi groups (all p- values > 0.05, Supplemental Material). In the Campanian Gobi, the non-avian theropod median CCM2 (59.91%) and the bird median CCM2 (28.25%) are significantly lower than in the Jehol, whereas the squamate median CCM2 in the Gobi (53.67%) is comparable to that seen in the Jehol (55.17%). 162 5.2.4. Continental-scale influence of exceptional preservation on phylogenetic character data To examine the effects of lagerstätten-style fossil preservation on phylogenetic information content in the fossil records of continents, I performed several pairwise statistical comparisons between median CCM2 percentages (Mann-Whitney U) and cumulative distribution (Kolmogorov-Smirnov) in the fossil records of non-avian theropods, birds and squamates in Asia with and without the Jehol and Gobi assemblages (Fig. 3A-C). I recovered different patterns of the influence of the Jehol Biota and Djadokhta/Baruungoyot formations on CCM2 distributions of representative groups. For non-avian theropod dinosaurs, removing taxa found in the Jehol Biota does not significantly affect the median CCM2 value and distribution shape (Fig. 3A, Supplemental Material). Similarly, removing Gobi desert taxa has no significant effect on the distribution of CCM2 values of taxa found in Asia (Fig. 3A, Supplemental Material). In fact, removing all non-avian theropod taxa found in the Jehol Biota and Campanian Gobi Desert does not significantly affect the median CCM2 value or distribution shape of species CCM2 values in Asia (Fig. S2, Supplemental Material). For Mesozoic birds, removing taxa found in the Jehol Biota from the total dataset from Asia yields a median CCM2 value and a distribution of CCM2 values that are significantly lower (Fig. 3B). Conversely, removing Gobi desert taxa (n = 4) unsurprisingly has no significant effect on the distribution of CCM2 values of taxa found in Asia (Fig. 3B, Fig. S5, Supplementary Information). The patterns observed in the continental record of Asia for squamates is the inverse of that seen in birds (Fig. 3C). In removing the squamate taxa found in the Jehol Biota (n = 7), I unsurprisingly recover a distribution of CCM2 values that are not statistically significantly different from the total dataset. If I remove the taxa found in the Gobi Desert assemblage, the median CCM2 value 163 becomes significantly lower, and the distribution shape of CCM2 values also decreases significantly (Supplemental Material). 5.2.5. Incorporation of lagerstätten taxa into phylogenetic analyses The patterns in CCM2 distributions and taxonomic abundance in non-avian theropods, birds and squamates found in the Jehol Biota and the Campanian Gobi Desert may play a role in how these taxa are incorporated into phylogenetic analyses (Fig. 3D-I). In non-avian theropods (Fig. 3D, G), the taxa from Jehol Biota and Djadokhta/Baruungoyot incorporated into the Theropod Working Group (TWiG) dataset (O’Connor et al., 2020) are roughly equal in terms of families/lineages represented (Gobi Desert: 13; Jehol: 11) and the percentage of total taxa used in the analysis (Gobi Desert: 11.19%; Jehol: 12.90%). For the avian dataset (Fig. 3E, H), 9 families and 31.04% of avian taxa used in the TWiG dataset are derived from the Jehol Biota, while only one taxon from the Djadokhta/Baruungoyot formations is incorporated into the TWiG dataset. For the squamate phylogenetic analyses (Gauthier et al. 2012 [GEA] and Simões et al. 2018 [SEA], Fig. 3F, I, Figure S3), no taxa from the Jehol are incorporated into the GEA analysis, while only 1 taxon, Dalinghosaurus longidigitus, is incorporated in the SEA analysis. Conversely, the assemblage in the Djadokhta/Baruungoyot formations contributes the most families/lineages represented (GEA: 11; SEA: 7) and the highest percentage of fossil taxa incorporated into the analysis (GEA: 45.01%; SEA: 40.91%) compared to any other assemblage in the squamate fossil record. 5.2.6. The phylogenetic “lagerstätten effect” in a global sampling context Out of landmasses that have sample sizes ≥ 6 species of non-avian theropods, Mesozoic birds, and squamates, respectively, the record from Asia contains the highest median CCM2 percentage (Fig. 4, S4, S5, Supplemental Material). I ran an additional set of pairwise 164 statistical tests to assess the significance of these observed differences. In the global record of phylogenetic information preserved in non-avian theropods (Fig. 1, S4), the median CCM2 and distribution shape is significantly different from that of Africa, Europe, and South America. There are also no significant differences in the distributions found in the well-sampled theropod- bearing units of North America, as well as Australasia, India, and Madagascar, although the lack of difference between the latter three may be due to their small sample size (Fig. S4, Supplemental Material). Thus, the signal from preserved phylogenetic information in non- avian theropod assemblages in the Jehol Biota and Campanian Gobi Desert is not only lost in the well-sampled and highly complete record from Asia, but is also lost in a global context due to the well-sampled, highly complete record from North America which contributes to a fossil record that preserves a significantly higher amount of phylogenetic information relative to birds and squamates (Fig. 1D). Further interrogation of this pattern is needed and warranted, but is beyond the scope of the current study. When bird taxa found in the Jehol Biota are removed from the Asia dataset (Fig. 2B), a significantly lower distribution of CCM2 values is recovered, such that the median CCM2 value and distribution shape are statistically indistinguishable from the CCM2 distributions of most landmasses, except for the highly incomplete record in North America (Fig. S5, Mann-Whitney U: p = .0081; Kolmogorov-Smirnov: p = 0.0034). This illustrates the outsized impact of this unique Jehol avian assemblage on the preservation of phylogenetic character data in Asia, which in turn strongly influences the distribution of phylogenetic information in the global fossil record of Mesozoic birds. The outsized effect that the Jehol Biota has on the completeness of our understanding of Mesozoic bird evolution has been examined in detail in numerous studies (e.g., Brocklehurst et al., 2012, Zhou, 2014; Chiappe & Qingjin, 2016), as has the effects of multitudes 165 of hypoxic lacustrine lagerstätten deposits on our understanding of fossil terrestrial ecosystems (Smith et al., 2019; Grande 2013; Chiappe & Qingjin, 2016; Allen et al., 2020). The remainder of the results section will focus on the novel findings from the squamate fossil record and the aeolian deposits of the Campanian Gobi Desert. The left panel of Figure 4 displays the distribution of CCM2 percentages for eight landmasses in order of increasing median value of fossil squamate species. Pairwise statistical comparisons between median CCM2 percentages (Mann-Whitney U) and cumulative distribution (Kolmogorov-Smirnov) among landmasses show no statistically significant differences, with only one notable exception in the data obtained from Asia (Fig. 4, Supplemental Material). For all fossil squamate species found in Asia, the median CCM2 percentage and the cumulative distribution shape of CCM2 percentages are statistically significantly different from all other landmasses, except for Madagascar and Australasia (0.05 > p > α). 5.2.7. Depositional setting and fossil squamate completeness Pie charts illustrating the relative abundance of fossil squamate species found in different depositional environments are shown on the right-hand side of the violin plots of the CCM2 distributions for landmasses in Figure 4. The distribution of CCM2 values per depositional environment with 17 or more sampled fossil squamate species are shown on the right-hand panel of Figure 4. Pairwise statistical comparisons between median CCM2 percentages (Mann- Whitney U) and cumulative distribution (Kolmogorov-Smirnov) among these distributions reveal several patterns (Supplemental Discussion), but most importantly, the median and distribution shape of CCM2 percentages of fossil squamate species found in aeolian environments is statistically significantly different from every other surveyed environment apart 166 from the median marine CCM2 value. The cause for this discrepancy is almost certainly due to the presence of 50 highly complete lizard species sampled from the Upper Campanian Djadokhta and Baruungoyot aeolian deposits in Mongolia and China. Indeed, if I remove these taxa from the Asia sample, the distribution shape and median value do not showcase any statistically significant differences from the rest of the sampled landmasses (all p-values > α, except for the comparison of median CCM2 of Asia and India, p = 0.00013, Supplemental Material). The squamates found in the Late Cretaceous Gobi Desert demonstrate the profound effects that cases of exceptional preservation of phylogenetically-relevant characters (versus e.g., soft tissues or extreme abundance) have on fossil record completeness on continental and global scales. 5.2.8. Gobi Desert squamates compared to Lagerstätten deposits I acknowledge that most depositional environments in Figure 4 do not contain examples of exceptionally preserved squamate fossils. Therefore, I also compared the completeness of the Gobi Desert squamate assemblage to all other squamate assemblages found in deposits classified in some form or another as lagerstätten (Fig. 5, S6, Supplemental Material). While the Smoky Hill Chalk (Fig. 5A, n = 8) and lagoonal lagerstätten deposits (Fig. 5B, n = 10) do not have sufficient sample sizes of fossils for meaningful statistical comparison, I was able to compare the 50 Gobi desert squamates (Fig. 5E) to the squamate assemblages from the Eocene/Oligocene Quercy Phosphorites in France (Fig. 5C, Konzentrat-lagerstätte; n = 44) and squamates collectively found in Upper Cretaceous and Eocene lacustrine Konservat-lagerstätten deposits ( Fig. 5D, n = 35). The median CCM2 percentages, and distributions for these three lagerstätten types are statistically significantly different from one another (Supplemental Material), with the Quercy Phosphorites representing a diverse but highly incomplete squamate assemblage, the 167 Gobi Desert squamate assemblage being diverse and relatively complete, and the lacustrine lagerstätten representing highly complete but not as taxonomically diverse assemblages. 5.3. Discussion 5.3.1. The desert dunes of the Campanian Gobi Desert: a different kind of taphonomic anomaly? Significant differences are present in the preserved amount of phylogenetic information in the fossil record of non-avian theropods, Mesozoic birds, and squamates at the global level (Fig. 1D) and in the Jehol lacustrine konservat-lagerstätte (Fig. 2A). Conversely, and perhaps surprisingly, in the aeolian deposits of the Campanian Gobi Desert, I found a lack of statistically significant difference in the preservation of phylogenetic character data in squamates, non-avian theropods and birds (Fig. 2B). Given the global context of the extreme statistical differences between the phylogenetic information preserved in the record of non-avian theropods and squamates (Fig. 1D, Supplemental Material), I interpret these results from the Djadokhta/Baruungoyot to be the product of uniform preservation and/or collection of phylogenetically-relevant information. This uniformity in phylogenetic completeness could be due to the unique preservation potential in aeolian sedimentary environments, such as immediate burial during large dune collapses and/or relatively quick burial during major sandstorms (Dashzeveg et al., 1995 ; Dashzeveg et al., 2005). On the other hand, the rich, 100-year history of intense sampling and research interest in the Djadokhta/Baruungoyot formations (Currie, 2000) could lead to the theropod, bird and squamate records reaching their maximized potential for preservation and completeness in an aeolian depositional setting. Interestingly, the median CCM2 value and distribution of CCM2 percentages for Campanian Gobi Desert squamate species is extremely high when compared to the global 168 distribution (p <<< 0.05, Fig. 1D, 2B Supplemental Material), while there is a lack of statistical difference observed in the median CCM2 value and distribution of CCM2 percentages for Campanian Gobi Desert non-avian theropods and birds relative to their global distribution (Fig. 1D, 2B, Supplemental Material). This differs from the pattern seen for the Jehol (Fig. 2A, Supplemental Material), in which the CCM2 distributions of all three groups are significantly higher than the global distributions, demonstrating widespread exceptional preservation of phylogenetic information. Despite the differences between the Gobi/Jehol CCM2 distributions relative to the global records, it is noteworthy that the median CCM2 percentage and CCM2 distribution shape for squamates in the Jehol and Gobi Desert are not statistically significantly different from one another (Supplemental Material). The small sample size of described species from Jehol might be to blame for this pattern, but even when comparing the Campanian Gobi Desert squamates to all described squamate species from lacustrine lagerstätten deposits (Fig. 5D, E, Supplemental Material), the differences in median CCM2 (Gobi: 53.67%; Lacustrine Lagersätten: 65.39%) value are not outlandishly different from one another, even if they are statistically significantly different (Supplemental Material). Taken together, I interpret these results as evidence of lagerstätten-type exceptional preservation of phylogenetic information in at least the squamate fossil record from the aeolian deposits of the Djadokhta and Baruungoyot formations. 5.3.2. The “lagerstätten effect” on taxon selection in phylogenetic analyses: supply vs. demand I have shown that the preservation of phylogenetic information among different groups in a fossil assemblage can be both non-uniform (as seen in the Jehol Biota, Fig. 2A) and uniform (as seen in the Campanian Gobi Desert, Fig. 2B). I have also shown that the continental (Fig. 3A-C) and global (Fig. 4, S4, S5, Supplemental Material) effects of exceptional preservation of 169 phylogenetic information in a fossil assemblage can be different depending on the quality of the fossil record of individual constituent groups (Fig. 1). These results also show that there can be differing effects on taxon selection in phylogeny (Fig. 3D-I) by exceptionally-preserved fossil assemblage constituents from a given geological unit (or units, as in the Jehol and Campanian Gobi) depending on the quality of their respective fossil records. In non-avian theropods, which preserve by far the highest amount of phylogenetic data of the three groups and showcase more complete records on multiple continents, the Jehol and Campanian Gobi Desert contribute nearly equally to the total number of taxa used in the TWiG dataset (Fig. 3D,G). The presence of numerous, highly phylogenetically-complete taxa, both in Asia outside of the Jehol/Campanian Gobi Desert assemblages and in North America suggests that there is a high-quality supply of theropod taxa from the global dataset, such that there is less demand to incorporate a larger portion of the 62 non-avian theropod taxa described from the Jehol and the Campanian Gobi Desert into broad phylogenetic analyses. Therefore, interpretations of the phylogenetic relationships of non-avian theropod dinosaurs may be less vulnerable to biases related to the “lagerstätten effect” than in Mesozoic birds and squamates. The global preservation of phylogenetic information in the fossil record of Mesozoic birds is significantly poorer than that of non-avian theropods (Fig. 1D, Brocklehurst et al., 2012). This means that there is proportionally a less high-quality supply of bird fossils to assess phylogenetic relationships, therefore increasing the demand on the taxonomically and phylogenetically diverse Jehol bird assemblage to provide structure to the Mesozoic bird Tree of Life. This bias is apparent with 31.04% of the avian portion of the TWiG dataset being made up of Jehol taxa (Fig. E), by far the largest contribution of any Mesozoic bird assemblage. The Campanian Gobi Desert avian assemblage is represented in the TWiG dataset by a single taxon, 170 Gobipteryx, reflecting the lack of “lagerstätten effect” generated from the small but relatively complete bird taxa therein. These results corroborate previous assessments of the outsized effect that the diverse assemblage of fossil birds in the Jehol exerts over the Mesozoic avian fossil record (Brocklehurst et al., 2012; Chiappe & Qingjing, 2016). Despite having the largest sample size (n = 797) and spanning the widest range of geologic time (Middle Triassic to Late Pleistocene) of the three surveyed groups, the fossil record of squamates contains a distribution of CCM2 values with the lowest median value (11.38%, Fig. 1) and a high concentration of species with CCM2 scores below 20% (522 out of 797 taxa). Similarly to Mesozoic birds, this means that the squamate fossil record contains a relatively small supply of more phylogenetically-complete fossils to incorporate into phylogenetic analyses, thus increasing demand on deposits of exceptional preservation to fill out the structure of the squamate Tree of Life in geologic time (Fig. 3F,I, Fig. 5). Even though there can be an abundance of taxa and remarkable diversity of species in other lagerstätten deposits containing squamates (Fig. 5), the unique combination of fossil lizard taxonomic and phylogenetic diversity from the Campanian Gobi Desert meets the demand of filling gaps in a largely incomplete fossil record by providing structure to numerous branches from disparate portions of squamate phylogenetic trees (Fig. 3I, Fig. 5E, Fig. S7). Thus, in terms of preserved phylogenetic information content, the Campanian Gobi Desert represents an aeolian lagerstätten deposit that profoundly effects the global picture of squamate fossil record completeness (Fig.4), and the deep-time structure of squamate evolutionary relationships (Fig. 3I, Fig. 5). 5.3.3. Quantifying the “lagerstätten effect” via a phylogenetic lens Quantifying formation-specific preservation of phylogenetic information in multiple organismal groups provides a novel comparative lens through which to assess the effects of 171 exceptionally preserved fossil assemblages on our interpretations of the Tree of Life. Comparing the amount of phylogenetic information in the fossil records of non-avian theropod dinosaurs, Mesozoic birds, and squamates revealed the potential for higher resilience to the “lagerstätten effect” in the more complete record of non-avian theropods, as well as corroborating previous observations of how much our understanding of the Mesozoic bird fossil record is filtered through the diverse Jehol assemblage. But most strikingly, in surveying the completeness of the global fossil record of squamates, I found that the assemblage of 50 highly complete species of lizard from the Upper Cretaceous Djadokhta and Baruungoyot formations of the Gobi Desert exert an anomalously large influence over the availability of phylogenetic character data, as well as taxon selection in phylogenetic analyses. The unexpected findings from aeolian-dominant facies also show that the potential to preserve a high quantity and quality of evolutionary information is not necessarily restricted to traditional lagerstätten-style depositional settings. These patterns invite us to consider other overlooked sedimentological regimes as candidates for exceptional preservation of phylogenetic information. Quantifying the “lagerstätten effect” through this phylogenetic lens expands our capacity to maximize the extraordinary wealth of existing paleobiological information available in the rock record. But perhaps more critically, assessing the evolutionary value of exceptional preservation helps parameterize gaps in the fossil record that we can prioritize in future sampling endeavors, improving our understanding of biological patterns through time and space. 5.4. Materials & Methods Taxonomic, stratigraphic, and occurrence-based data from the published squamate fossil record were downloaded from the Paleobiology Database (PBDB). I limited the sampled data to the species level, as both phylogenetic datasets used in this study (Gauthier et al., 2012 [GEA]; 172 Simões et al., 2018 [SEA]) use species as their operational taxonomic units. The dataset includes 797 extinct species (Fig. 1A) and 16,983 specimens from 469 localities that range from the Middle Triassic (Anisian) to the late Pleistocene in age. PBDB information for each species was vetted using 492 published specimen and locality descriptions (See Supplemental Material). Additionally, for comparisons in the Gobi Desert assemblage, I incorporated previously- published skeletal completeness assessments for 402 species of non-avian theropods (Cashmore & Butler 2019) and 128 species of Mesozoic birds (Brocklehurst et al. 2012). To assess the completeness of the global fossil record of squamates, I used the Character Completeness Metric 2 (CCM2, Mannion & Upchurch, 2010), which measures the percentage of phylogenetic characters that can be scored for all specimens referred to a fossil species (Fig. 1). I used two datasets that represent competing morphology-based hypotheses of squamate evolutionary relationships (GEA and SEA, Fig. S1). I combined these two datasets and removed overlapping characters for a total of 860 scorable phylogenetic characters. Individual species’ completeness was scored based on the presence of individual skeletal elements for which a corresponding portion of the combined phylogenetic characters could be scored. I carried out scoring species’ CCM2 percentage by using only the characters that the species could be scored for. For instance, many fossil snake and amphisbaenian species do not possess limbs (i.e., no matter how complete the skeletal remains are, these species would always be missing 150 characters of the limbs and limb girdles). Because of this disparity, I measured legless squamate taxa’s “True Completeness” out of 710 characters instead of the 860 I used for squamates with four limbs. For the non-avian theropod dataset (Cashmore & Butler 2019), I converted previously- assessed Skeletal Completeness Metric 2 (SCM2) values to CCM2 values using a character 173 matrix assessing higher-level relationships of theropod dinosaurs (Smith et al., 2007) and a recent iteration of the Theropod Working Group (TWiG) character matrix assessing the relationships of coelurosaurs (O’Connor et al., 2020). I incorporated the Mesozoic bird CCM2 dataset assessed by Brocklehurst et al. (2012) as-is. 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A) Heat map of non-avian theropod phylogenetic character density across the skeleton of an example theropod, Teratophoneus curriei, (Carr et al., 2011) on public display at the Natural History Museum of Utah. B) Heat map of avian phylogenetic character density across the skeleton of an example Mesozoic bird, Archaeopteryx lithographica (Meyer 1861), on public display at the Natural History Museum of Los Angeles County. C) Heat map of character density across an example squamate skeleton (Uta stansburiana). D) Summary violin plots for the phylogenetic completeness (CCM2) of described species in the global fossil record of non-avian theropods (top), Mesozoic birds (middle) and squamates (bottom). White dot: median; black bar: interquartile range; black line: 95% confidence interval. 179 Figure 2. Comparisons of species phylogenetic completeness of non-avian theropod dinosaurs, birds, and squamates preserved in the lacustrine konservat-lagerstätten deposits of the Yixian and Jiufotang formations (Jehol Biota) and the aeolian lagerstätten deposits of the Djadokhta and Baruungoyot formations (Campanian Gobi Desert). A) Left: Paleogeographic map showing Barremian/Aptian Asia (with the location of Liaoning Province outlined). Modified from Scotese (2016) using GPlates software (Müller et al. 2018). Right: violin plots comparing distributions of species completeness (CCM2) values among non-avian theropods, birds and squamates represented in the Barremian/Aptian Jehol Biota assemblage. B) Left: Paleogeographic map showing late Campanian Asia (with the location of modern Mongolia outlined). Modified from Scotese (2016) using GPlates software (Müller et al. 2018). Right: Violin plots comparing distributions of species completeness (CCM2) values among non-avian theropods, birds and squamates represented in the Late Cretaceous (Campanian) Djadokhta and Baruungoyot Formation assemblages. White dot: median; black bar: interquartile range; black line: 95% confidence interval. 180 Figure 3. Comparisons of continental-scale differences in the effects of lagerstätten deposits (Djadokhta, Baruungoyot formations; Jehol Biota) on the preservation of phylogenetic character data. A) Distribution of all non-avian theropod CCM2 values in Asia (top), and distribution of CCM2 values when removing taxa from the Lower Cretaceous Jehol Biota (middle, violet background) and Campanian Gobi Desert (bottom, coral background). B) Distribution of all Mesozoic bird CCM2 values in Asia (top), and distribution of CCM2 values when removing taxa from the Lower Cretaceous Jehol Biota (middle, violet background) and Campanian Gobi Desert (bottom, coral background). C) Distribution of all fossil squamate CCM2 values in Asia (top), 181 and distribution of CCM2 values when removing taxa from the Lower Cretaceous Jehol Biota (middle, violet background) and Campanian Gobi Desert (bottom, coral background). White dot: median; black bar: interquartile range; black line: 95% confidence interval. D) Summary of the number of non-avian theropod families represented from the Jehol Biota assemblage on the Theropod Working Group (TWiG) phylogeny. E) Summary of the number of avian families represented from the Jehol Biota assemblage on the Theropod Working Group (TWiG) phylogeny. F) Summary of the number of squamate families represented from the Jehol Biota assemblage on the GEA phylogeny. G) Summary of the number of non-avian theropod families represented from the Djadokhta/Baruungoyot assemblage on the Theropod Working Group (TWiG) phylogeny. H) Summary of the number of avian families represented from the Djadokhta/Baruungoyot assemblage on the Theropod Working Group (TWiG) phylogeny. I) Summary of the number of squamate families represented from the Djadokhta/Baruungoyot assemblage on the GEA phylogeny. 182 Figure 4. Summary of the effects of regional sampling and depositional setting on the amount of available phylogenetic information in the squamate fossil record. Left: violin plots of the distribution of squamate Character Completeness Metric 2 (CCM2) percentages per landmass. Not displayed: Antarctica (n =2); Caribbean (n = 3). Pie charts show the relative proportions of depositional environments in which fossil squamate species are found per corresponding landmass. Right: violin plots of the distribution of squamate CCM2 percentages per depositional setting (right). White dot: median; black bar: interquartile range; black line: 95% confidence interval. 183 Figure 5. Summary of distributions of Character Completeness Metric 2 (CCM2) values for squamates found in established lagerstätten localities, with a summary of the number of families represented in localities using the GEA phylogeny. A) Distribution of CCM2 values and number of families of squamates found in the Upper Cretaceous Smoky Hill Chalk. Example species: Platecarpus tympaniticus Konishi et al. 2015. B) Distribution of CCM2 values and number of families of squamates found in lagoonal lagerstätten deposits. Example species: Huehuecuetzpalli mixtecus Reynoso 1992. C) Distribution of CCM2 values and number of 184 families of squamates found in the Eocene/Oligocene Quercy Phosphorites. Example species: Necrosaurus cayluxi Augé 2005. D) Distribution of CCM2 values and number of families of squamates found in lacustrine lagerstätten deposits. Example species: Saniwa ensidens Rieppel & Grande 2007. E) Distribution of CCM2 values and number of families of squamates found in the Upper Cretaceous Djadokhta and Baruungoyot formations. Example species: Saichangurvel davidsoni Conrad & Norell 2007. 185 5S. Supplementary Information for Chapter 5 Depositional setting and completeness Pairwise statistical comparisons between median CCM2 percentages (Mann-Whitney U) and cumulative distribution (Kolmogorov-Smirnov) among these distributions reveal several patterns. First, the median and distribution shape of the CCM2 values from lacustrine environments differ from those seen in fluvial channel and karst environments. Second, the median and distribution shape of CCM2 values in karst environments also differs from those of marine and coastal lagoon depositional settings. Third, the median and distribution shape of CCM2 values in marine depositional environments are statistically significantly different from those found in all three fluvial depositional categories (fluvial floodplain, fluvial channel, fluvial indet.). Gobi Desert Lizards Compared to Other Lizards Fossil preservation can be dependent not only on depositional environment, but also body plan. Because only lizards have been described from the Djadokhta/Baruungoyot formations, it is important to consider their collective completeness compared alongside lizard fossils from other depositional settings with high completeness without the squamates with extremely different body plans (snakes, mosasaurs, amphisbaenians). If we compare the completeness of lizards found in the Late Cretaceous Gobi Desert to lizards found across geologic time in lacustrine and lagoonal environments (Fig. S3) we observe statistically significant differences in median CCM2 ( Gobi + Lacustrine: α = 0.05; p = 0.0022; Gobi + Lagoon: α = 0.05; p = 0.0002) and distribution shape (Gobi + Lacustrine:α = 0.05; p = 0.000019; Gobi + Lagoon: α = 0.05; p = 0.0017). These results show that even though we can expect the best physical preservation and most phylogenetically complete lizards (e.g., Saniwa ensidens in lacustrine settings with CCM2 = 186 96.28%; Huehuecuetzpalli mixtecus in lagoonal settings with CCM2 = 72.94%) in low-energy, potentially hypoxic or anoxic depositional settings, there can be a high average amount of phylogenetic information preserved in settings that do not meet those criteria (median CCM2 for Gobi desert: 54.65%; median CCM2 for lacustrine: 30.31%; median CCM2 for lagoonal: 35.08%). The Gobi Desert “lagerstätten effect” in the squamate fossil record The “lagerstätten effect” on phylogenetic data in the squamate fossil record can be characterized via several patterns. 1) Well-known konservat-lagerstätten deposits may have high preservation of squamate phylogenetic data, but the restricted geography and often limited temporal scope of these classic deposits likely contribute to less taxonomic abundance compared to the Djadokhta and Baruungoyot formations (Fig. 5A, B, D); 2) the Gobi Desert squamate assemblage is significantly more complete than Konzentrat-lagerstätten deposits like the Quercy Phosphorites, and therefore has distinctively different preservation of phylogenetic character data even if higher-level taxonomic diversity is similar Fig. 5C, E); 3) Although lacustrine lagerstätten possess the highest median CCM2 percentages and have the most complete fossils, those deposits still contain less overall alpha diversity of squamates, which results in less taxa available to use in phylogenetic analyses than in the Gobi Desert aeolian deposits (Fig. 5D, E, Fig. 5A,D, Fig. S6). These patterns suggest that the Djadokhta and Baruungoyot formations exert an anomalously large influence on the preservation and availability of squamate phylogenetic character data in Asia, which in turn influences our understanding of squamate evolutionary relationships through time and space, regardless of phylogenetic dataset (Fig. 3, Fig. 3A, D, G, Fig. S6). In the future, phylogenetic comparative analyses could test that if one removed fossil 187 squamate taxa found in the Djadokhta and Baruungoyot formations from phylogenetic datasets, there might be a huge deficit in our understanding of divergence times of both fossil and extant squamate lineages. Even without such tests, the observations and analyses presented in this study show that the highly diverse an exceptionally complete squamate assemblage of the Djadokhta and Baruungoyot formations represents an extreme case of the “lagerstätten effect” on the completeness of the global fossil record of an organismal group The extremities observed in the continental influence of the fossil record of squamates and birds from the Djadokhta/Baruungoyot formations and Jehol Biota could be a product of sample size (Gobi squamates: n = 50; Jehol squamates: n = 7; Gobi birds: n = 4; Jehol birds: n = 25). However, the high CCM2 values and high percentages of the total species sampled in this study (Gobi: 6.18% of species; Jehol: 4.97% of species; n = 1327) suggests that these discrepancies might not be entirely related to sampling bias in the fossil record. The lack of sampling biases and high completeness could suggest that these discrepancies instead reflect an approximation of the actual taxonomic makeup of these fossil communities, and that the Gobi Desert and Jehol lagerstätten communities truly reflect biodiversity hotspots for squamates and birds, respectively. The non-avian theropod record happens to be highly diverse and highly complete from both the Djadokhta/Baruungoyot formations and Jehol Biota. This could reflect the ubiquity of theropods as key components of Mesozoic terrestrial ecosystems (Cashmore & Butler, 2019) around the globe, or a true bias in sampling due to asymmetrical research interests among workers (Benton, 2008, 2010). Another explanation for the high completeness of squamates and birds is that the preservation conditions (Jehol: hypoxic/anoxic lacustrine environment, Zhou, 2014; Gobi: immediate burial from dune collapses, Dashzeveg et al. 1995) favored smaller-bodied tetrapods. 188 Although small-bodied taxa make up the majority of species examined here, the presence of larger-bodied lizards such as Estesia mongliensis (Norell et al., 1992) in the Djadokhta/Baruungoyot formations, and the high completeness of giant non-avian theropods in the Jehol Biota such as Yutyrannus (Xu et al., 2012) and Sinotyrannus (Ji et al., 2009) suggest that selective preservation based on small body size is not a ubiquitous taphonomic feature of these units. These results show that even if depositional units exhibit uniform exceptional preservation, the “lagerstätten effect” exerted by that unit on global evolutionary information can be remarkably different depending on the organismal group in question. The methods outlined in this study offer a quantitative characterization of this phenomenon in multiple taxonomic groups and multiple lagerstätten deposits. 189 SUPPLEMENTARY FIGURES Figure S1. Summary of morphology-based hypotheses of squamate evolutionary relationships, whose character datasets were used for the Character Completeness Metric 2 (CCM2) in this study. A) Gauthier et al. (2012) hypothesis. B) Simões et al. (2018) hypothesis. Silhouettes with colored outlines indicate major squamate groups whose phylogenetic positions differ significantly among the two hypotheses. All silhouettes traced from publicly available images at www.phylopic.org. 190 Figure S2. Distribution of Character Completeness Metric 2 (CCM2) in non-avian theropod dinosaurs from the total Asia dataset (top) and without the 62 surveyed taxa from the Jehol Biota and Campanian Gobi Desert (bottom). 191 Figure S3. Comparisons of squamate families represented in the Gauthier et al. (2012) and Simões et al. (2018) datasets from the Jehol Biota (top) and Campanian Gobi Desert (bottom). 192 Figure S4. Violin plots of the distribution of non-avian theropod CCM2 values per sampled landmass. 193 Figure S5. Violin plots of the distribution of Mesozoic bird CCM2 values per sampled landmass. Not pictured: Antarctica (n = 2); Australasia (n = 1); Madagascar (n = 1). 194 Figure S6. Comparisons of distributions of fossil lizard CCM2 values from high-preservation potential depositional environments. 195 Figure S7. Comparisons of squamate families represented in the Gauthier et al. (2012) and Simões et al. (2018) datasets from each lagerstätten deposit surveyed in this study. A. Smoky Hill Chalk. B. Lagoonal lagerstätten deposits. C. Quercy Phosphorites. D. Lacustrine lagerstätten deposits. E. Djadokhta and Baruungoyot Formations. 196 Supplementary data Supplementary Data S1. Excel spreadsheet of taxon, specimen, and locality information from the Paleobiology Database and from primary literature. 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Proceedings of the Royal Society of London (9):273-273. 239 Scanlon, J. D., and B. S. Mackness. 2001. A new giant python from the Pliocene Bluff Downs Local Fauna of northeastern Queensland. Alcheringa 25(4):425-437. Smith, M. J. 1976. Small fossil vertebrates from Victoria Cave, Naracoorte, South Australia. IV. Reptiles. Szyndlar, Z. 1984. Fossil snakes from Poland. Acta Zoologica Cracoviensia 28(1 (1)). 240 CHAPTER 6: CONCLUSIONS Investigating the quality of phylogenetic information in the incomplete fossil record of squamates reveals a novel approach for interrogating the relationship between taphonomic/sampling filters and our ability to reconstruct the evolutionary relationships of fossil organisms in Deep Time. The methods and results presented in this dissertation provide a combination of analytical tools that have not only yielded new perspectives on the correlation between taphonomic & sampling biases and phylogenetic patterns in squamates, but also provide a strong basis for characterizing and quantifying these patterns across multiple taxonomic groups and sedimentological regimes on regional and global scales. Here, I will summarize the aims and outcomes of each dissertation chapter, as well as highlight future directions that each chapter has been, or will be taken in current and future projects. 6.1. Chapter 2 Review 6.1.1. Summary In Chapter 2, I broadly characterized the patterns in quality of phylogenetic information in 242- million-year fossil record of squamates. The characteristic incompleteness of their global fossil record means that teasing out higher-order biases related to depositional environment (i.e., geological bias) and regional sampling intensity (i.e., sampling bias) are difficult to complete, with a few exceptions found in lagerstätten (See 6.4. Chapter 5 Review). Instead, the most prevalent first-order filter on preserved phylogenetic information appears to be differences in how we sample the skeletons of squamates with different body plans. Mosasaurs have the highest level of phylogenetic completeness of any squamate group, which could be a product of their large body size (easier to spot in outcrop with the naked eye), unique morphology among 241 contemporary marine tetrapods, and/or the high preservation potential of the depositional environments in which their fossils are found (low-energy marine settings). Amphisbaenians have the second-highest phylogenetic completeness of the sampled squamate groups, which can almost certainly be attributed to the unique morphology and fusion of the character-dense elements in their skull, lending themselves to higher preservation potential. Lizards are the most abundant and morphologically diverse group sampled in this study, but their record overall is phylogenetically incomplete and extremely biased toward marginal tooth-bearing elements in the skull. Finally, with only a few exceptions, the snake fossil record is uniformly incomplete, and almost entirely consists of vertebrae, which are some of the least character-dense regions of the squamate skeleton. In describing the patterns in the preservation of phylogenetic data in the rich, but incomplete fossil record of squamates, I have identified key, morphology-based gaps in our understanding of their evolutionary history to target in future sampling endeavors. 6.1.2 Future Directions Results in Chapter 2, which are entirely based on published descriptions and associated locality data of species-level taxa, originate from perhaps the most highly filtered sampling tier of fossil anatomical data (Tiers 3 & 4, Figure 1). Published descriptions of squamate fossils usually can be categorized into one of three publication types: 1) First occurrences of specific taxa; 2) exceptionally complete specimens; 3) summary of a fossil squamate fauna in a particularly well-sampled region or specific geologic unit. This excludes a vast amount of fossil data in museum collections (Tier 2, Figure 1), which is subject to its own set of filters from data collected in the field and rock record. A comparison of the effects of anthropogenic sampling filters on our understanding of the fossil squamate anatomy and associated phylogenetic character data is the next logical step in understanding the biases present in museum collections. 242 Additionally, comparison to other taxonomic groups, both in vertebrates and in invertebrates that preserve in disarticulated parts, could reveal universal aspects of the biases that filter anatomical and phylogenetic data in the fossil record of animals. 6.2. Chapter 3 Review 6.2.1. Summary In Chapter 3, I provided an updated evaluation of the fossil record of squamates from a critical locality in our understanding of terrestrial ecosystems in the Late Campanian Western Interior of North America: the “Hunter Wash Local Fauna” in the Fruitland and Kirtland formations in Northwest New Mexico. The updated assemblage of squamates includes incomplete specimens referable to Chamopsiidae, Scincomorpha, Anguidae, Odaxosaurus, and Serpentes, as well as the first occurrence of a Platynotan lizard in the “Hunter Wash Local Fauna”. The presence of these taxa in the Fruitland/Kirtland formations align with observed squamate taxonomic diversity in other Upper Campanian North American sedimentary basins and adds key biogeographic data to our growing understanding of squamate diversity in the Cretaceous. The impactful biological data yielded from fragmentary specimens sampled directly from the field (Tier 1, Figure 1) highlight the importance of continued field-based collections work, and highlight the need for further analytical work that establishes parameters for incorporating incomplete fossils into broad biological and ecological studies. 6.2.2. Future Directions The results presented in Chapter 3 are part of a broader effort to describe and update the squamate fauna from Laramidia. While major strides were made in modernizing our understanding of the Late Campanian Laramidian squamate fauna in the last 20 years (e.g., Nydam 2007; Nydam & Voci, 2007; Nydam & Fitzpatrick, 2009; Nydam, Caldwell & Fanti, 243 2010; Nydam 2013a; 2013b, Nydam, Rowe & Cifelli, 2013), many important specimens remain undescribed, and most described squamate species from Late Campanian Laramidia need more rigorous placement into a geological, ecological, and phylogenetic context. Current projects I have undertaken related to this issue are 1) the description of material belonging to large-bodied lizard taxa in the Upper Campanian Kaiparowits Formation in southern Utah, USA; and 2) detailed revision of the extremely common and long-lived genus Chamops. Results from these studies will be placed into a broader dataset of tetrapods, plants, and paleoclimate proxy data to understand latitudinal biodiversity trends in a greenhouse world. 6.3. Chapter 4 Review 6.3.1. Summary In Chapter 4, I found that the fossil squamate record is biased in representation across the skeleton, and could affect our ability to place fossil squamate species into phylogenetic analyses. In particular, the fossil skeletal record of squamates is biased heavily towards marginal tooth-bearing elements of the skull (the upper and lower jaws), vertebrae, and ribs, while the rest of the bones in the skeleton are comparatively underrepresented in museum collections. With this data, I used novel applications of phylogenetic comparative methods to demonstrate that the biased (i.e., incomplete) fossil record is less likely to mislead our interpretations of squamate evolutionary relationships. Results like these are exciting, because they increase the scientific value of incomplete specimens housed in museum collections, and they allow us to include more of Earth’s extinct biodiversity as we piece together the past. More importantly, these methods lay a significant foundation for exploring these types of questions in the fossil records of other organismal groups that preserve disarticulated parts and potentially biases representation. 244 6.3.2. Future Directions By testing the reliability of the preserved phylogenetic information in the global fossil record, we may be able to incorporate a broader diversity of “incomplete” fossils into our assessments of fossil taxa and their evolutionary relationships (Figure 1). A more inclusive assessment of evolutionary relationships among extinct taxa will increase the footprint of paleobiological analyses, and may reveal hidden biological patterns in the past that otherwise would have been overlooked. This philosophy can be used broadly in future assessments of the reliability of phylogenetic information in the fossil records of ecologically important marine invertebrates (e.g., echinoids, corals), as well as prominent terrestrial vertebrate groups (e.g., birds, mammals). This type of research is relevant to both paleobiologists and modern biologists and ecologists, as improving the scientific power of the fossil record can provide critical contextual data for understanding current and future biotic crises and patterns. 6.4. Chapter 5 Review 6.4.1. Summary In Chapter 5, I use an established skeletal completeness metric to quantify the “lagerstätten effect” on the preservation of phylogenetic data in the global fossil record of non-avian theropod dinosaurs, Mesozoic birds, and squamates (e.g., lizards, snakes). I show that incomplete fossil records (e.g., Mesozoic birds, squamates) are more susceptible to the “lagerstätten effect” on phylogenetic data, which filters our interpretations of evolutionary relationships through exceptionally preserved taxa in one or two geologic units. Unexpectedly, I found that the aeolian deposits of the Late Cretaceous Gobi Desert of Mongolia and China preserve exceptionally complete lizard anatomical and phylogenetic data, such that those deposits exert an anomalously large influence on patterns of squamate fossil record completeness on global scales, and the 245 deep-time structure of squamate evolutionary relationships. These findings from aeolian- dominant facies demonstrate that the potential to preserve a high quantity and quality of evolutionary information is not necessarily restricted to traditional lagerstätten. Quantifying formation-specific preservation of phylogenetic information in multiple groups offers a novel comparative lens through which to assess the effects of exceptionally preserved fossil assemblages on our interpretations of the Tree of Life. 6.4.2. Future Directions Results in Chapter 5 quantify a fundamental pattern in the preservation of paleobiological information: that certain geological units hold an outsized influence on our understanding of the evolutionary history of a group (Figure 1). Determining the prevalence of this pattern among different animal groups will be an important next step for this line of inquiry. Of particular interest is determining the lagerstätten effect on phylogenetic information of marine invertebrates, which far outclass terrestrial vertebrates in terms of sheer number of specimens available to analyze. Given the results for a reduced lagertsätten effect on the more completely- sampled fossil record of non-avian theropod dinosaurs, it will be impactful to determine the “threshold” for how complete a fossil record needs to be sampled in order for the lagerstätten effect to be non-existent in the preservation of phylogenetic information. Future comparative work will be carried out using abundant and important marine invertebrate taxa, including scleractinian corals and echinoids. 6.5. Final Thoughts Despite the biases present in the incomplete squamate fossil record, much paleobiological information remains. Even fragmentary material lends itself well to regional paleobiogeographical comparisons in the Late Cretaceous Wester Interior of North America, and 246 can help fill crucial systematic and taxonomic gaps in distributions of squamate taxa. More critically, the results from analyses of phylogenetic signal in the squamate fossil record show that the information present in fossil squamate specimens is not more likely to mislead our interpretations of evolutionary relationships when compared to information that is missing. This is important to consider, as the incomplete squamate fossil record, and thus our understanding of squamate evolutionary relationships in deep time, are currently heavily filtered through the aeolian lagerstätten deposits of the Djadokhta and Baruungoyot formations in the Late Campanian Gobi Desert. By incorporating more incomplete (but trustworthy) fossil taxa into a phylogenetic framework, we can decrease the reliance on a single geologic unit for assessing the relationships of squamates through time. These findings come at a critical moment in the scientific discourse surrounding the higher-level evolutionary relationships of squamates. The incongruence between recovered higher-level phylogenetic relationships of squamates using molecular/combined- evidence data (Vidal & Hedges, 2009; Reeder et al., 2015; Simões et al., 2018) and morphological data (Conrad, 2008; Gauthier et al., 2012, Mongiardino-Koch & Gauthier, 2019) highlights the importance of further inquiry into the fossil record and incorporation of fossil taxa. This approach can fill in critical evolutionary gaps on long branches of the squamate tree of life, and document previously overlooked changes in character evolution that might have been discerned only from more complete fossils and/or extant taxa. References Conrad, J. L. 2008. Phylogeny and systematics of Squamata (Reptilia) based on morphology. Bulletin of the American Museum of Natural History 2008(310):1-182. 247 Gauthier, J. A., M. Kearney, J. A. Maisano, O. Rieppel, and A. D. B. Behlke. 2012. Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record. Bulletin of the Peabody Museum of Natural History 53(1):3-308, 306. Mongiardino Koch, N., and J. A. Gauthier. 2018. Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. PLoS One 13(8):e0202729. Nydam, R. L. 2013. Squamates from the Jurassic and Cretaceous of North America. Palaeobiodiversity and Palaeoenvironments 93(4):535-565. Nydam, R. L. 2013. Lizards and Snakes from the Cenomanian through Campanian of Southern Utah: Filling the Gap in the Fossil Record of Squamata from the Late Cretaceous of the Western Interior of North America. Pp. 370-423. In A. Titus, and M. Loewen, eds. At the Top of the Grand Staircase: The Late Cretaceous of Southern Utah. Indiana University Press, Bloomington, Indiana. Nydam, R. L., M. W. Caldwell, and F. Fanti. 2010. Borioteiioidean lizard skulls from Kleskun Hill (Wapiti Formation; upper Campanian), west-central Alberta, Canada. Journal of Vertebrate Paleontology 30(4):1090-1099. Nydam, R. L., J. G. Eaton, and J. Sankey. 2007. New taxa of transversely-toothed lizards (Squamata: Scincomorpha) and new information on the evolutionary history of “teiids”. Journal of Paleontology 81(3):538-549. Nydam, R. L., and B. M. Fitzpatrick. 2009. The occurrence of Contogenys-like lizards in the Late Cretaceous and Early Tertiary of the Western Interior of the USA. Journal of Vertebrate Paleontology 29(3):677-701. Nydam, R. L., T. B. Rowe, and R. L. Cifelli. 2013. Lizards and snakes of the Terlingua Local Fauna (late Campanian), Aguja Formation, Texas, with comments on the distribution of paracontemporaneous squamates throughout the Western Interior of North America. Journal of Vertebrate Paleontology 33(5):1081-1099. Nydam, R. L., and G. E. Voci. 2007. Teiid-like scincomorphan lizards from the Late Cretaceous (Campanian) of southern Utah. Journal of Herpetology 41(2):211-219. Reeder, T. W., T. M. Townsend, D. G. Mulcahy, B. P. Noonan, P. L. Wood Jr, J. W. Sites Jr, and J. J. Wiens. 2015. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa. PLoS One 10(3):e0118199. 248 Simões, T. R., M. W. Caldwell, M. Tałanda, M. Bernardi, A. Palci, O. Vernygora, F. Bernardini, L. Mancini, and R. L. Nydam. 2018. The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps. Nature 557(7707):706-709. Vidal, N., and S. B. Hedges. 2009. The molecular evolutionary tree of lizards, snakes, and amphisbaenians. Comptes rendus biologies 332(2-3):129-139. 249 Figures Figure 1. Summary of the flow of anatomical and phylogenetic information in the fossil record, outlined in this dissertation. In this study, I have quantified and characterized the various taphonomic and sampling biases that contribute to our understanding of the fossil record (purple), the effects that those biases have on phylogenetic character content (salmon), and the effects that those biases in phylogenetic information content have on our interpretations of evolutionary relationships.
Abstract (if available)
Abstract
While spectacularly-preserved fossils garner the most scientific and public attention, the majority of the world’s fossil collections are comprised of incomplete, fragmentary, and understudied specimens. These collections are treasure troves of paleobiological information, and, in particular, have the potential to be essential data in assessing the evolutionary relationships (i.e., phylogeny) of extinct organisms and their living relatives. Before uncritically incorporating these data into analyses, we must make targeted inquiries into whether the phylogenetic information retained in incomplete fossil specimens is systematically biased in some way. It remains an open question to what degree geological factors, taphonomic factors, and factors related to asymmetrical sampling among workers affect our ability to understand a group’s evolutionary history. In essence, we need to address not just what an imperfect/incomplete fossil record looks like, but also whether it can be trusted within a phylogenetic framework.
This study explores these issues using the >242 million-year fossil record of one of the most prominent groups in the modern vertebrate fauna: the Squamata (lizards, snakes, amphisbaenians, mosasaurs, and their relatives). Using: 1) novel applications of an established fossil skeletal completeness metric, as well as: 2) an assessment of skeletal anatomical representation in fossil squamate specimens observed in-person, in electronic collections databases, and the published literature, I aim to quantitatively characterize the geological, taphonomic and anthropogenic sampling biases that contribute to the assembly of a fossil record. I show that the global squamate fossil record, ranging in age from the Middle Triassic to the Late Pleistocene, preserves a highly incomplete amount of phylogenetic information on broad scales. This global pattern is also evident at local and regional levels, which I showcase in a description of new fossil lizard material in the Late Cretaceous of the Western Interior of North America. Anatomical biases are also present in the squamate fossil record, with marginal tooth-bearing bones (i.e., premaxillae, maxillae, dentaries) and vertebrae being overrepresented in global museum collections compared to the rest of the skeleton.
Given the incompleteness of the squamate fossil record, it is important to then test a question fundamental to paleobiology: how does incomplete preservation impact the phylogenetic information contained in the fossil record? I test this question by directly measuring the phylogenetic signal (i.e., how well the evolution of a trait aligns with a given evolutionary hypothesis) present in parts of the squamate skeleton that are both overrepresented and underrepresented in the fossil record. Parsimony- and model-based comparative analyses indicate that the most frequently-occurring parts of the squamate skeleton in the fossil record retain similar levels of phylogenetic signal as parts of the skeleton that are rarer. These results demonstrate that the biased squamate fossil record contains reliable phylogenetic information, and support our ability to place incomplete fossils in the Tree of Life.
Interrogating the reliability of phylogenetic information preserved in the incomplete squamate record is critical and timely, because our current understanding of squamate evolutionary relationships in Deep Time is filtered heavily through a single place and time. The extraordinarily diverse and complete lizard assemblage from the Campanian Djadokhta and Baruungoyot Formations of Mongolia and China exert an anomalously large influence on patterns of squamate fossil record completeness on global scales, and form a majority of the deep-time structure of squamate evolutionary relationships. As a result, the preservation of phylogenetic information in the global squamate fossil record is particularly susceptible to the “lagerstätten effect” in ways that more completely sampled fossil records, such as that of the non-avian dinosaurs, are not. By incorporating reliable phylogenetic information in incomplete squamate fossil species into analyses, we may be able to lessen the “lagerstätten effect” on our understanding of evolutionary relationships. Thus by addressing the taphonomic and sampling biases related to incomplete and exceptionally complete fossils, this study offers a novel phylogenetic framework to interrogate the quality of the fossil record, and introduces methods that can be applied to any fossil group of interest.
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Assessing the quality of the fossil record using a phylogenetic approach
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Woolley, Charles Henrik
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Assessing the quality of the fossil record using a phylogenetic approach
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Doctor of Philosophy
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Geological Sciences
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2023-05
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05/11/2024
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