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Downloaded From TAXONOMIC CHECKLISTS AS BIODIVERSITY DATA : HOW SERIES OF CHECKLISTS CAN PROVIDE INFORMATION ON SYNONYMY , CIRCUMSCRIPTION CHANGE AND TAXONOMIC DISCOVERY By GAURAV GIRISH VAIDYA B.Sc., National University of Singapore, 2006 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirement for the degree of Doctor of Philosophy Department of Ecology and Evolutionary Biology 2017 This thesis entitled: Taxonomic checklists as biodiversity data: how series of checklists can provide information on synonymy, circumscription change and taxonomic discovery written by Gaurav Girish Vaidya has been approved for the Department of Ecology and Evolutionary Biology Robert Guralnick J. Patrick Kociolek Date The final copy of this thesis has been examined by the signatories, and we find that both the content and the form meet acceptable presentation standards of scholarly work in the above mentioned discipline. Vaidya, Gaurav Girish (Ph.D., Ecology and Evolutionary Biology) Taxonomic checklists as biodiversity data: how series of checklists can provide information on synonymy, circumscription change and taxonomic discovery Thesis directed by Professor Robert Guralnick Taxonomic checklists are a fundamental and widely-used product of taxonomy, providing a list of recognized taxa within a taxonomic group in a particular geographical area. Series of taxonomic checklists provide snapshots of recognized taxa over a period of time. Identifying and classifying the changes between these checklists can provide information on rates of name, synonym and circumscription change and can improve aggregation of datasets reconciled to different checklists. To demonstrate this, I used a series of North American bird checklists to test hypotheses about drivers of splitting rates in North America birds. In particular, I asked if splitting was predominantly undoing previous lumping that happened during the heyday of the modern synthesis. I found that bird species have been split at an accelerating rate since the 1980s. While this was partially the result of previously lumped species being resplit, most splits were unrelated to previous lumps and thus represent new discoveries rather than simply the undoing of previous circumscription changes. I also used a series of North American freshwater algal checklists to measure stability over fifteen years, and found that 26% of species names were not shared or synonymized over this period. Rates of iii synonymization, lumping or splitting of species remained flat, a marked difference from North American birds. Species that were split or lumped (7% of species considered) had significantly higher abundance than other species in the USGS NAWQA dataset, a biodiversity database that uses these checklists as an index. They were associated with 19% of associated observations, showing that a small number of recircumscribed species could significantly affect interpretation of biodiversity data. To facilitate this research, I developed a software tool that could identify and annotate taxonomic changes among a series of checklists, and could use this information to aggregate biodiversity data, which will hopefully facilitate similar research in the future. My dissertation demonstrates the value of taxonomic checklists series to answer specific questions about the drivers of taxonomic change ranging from philosophical and technical changes to characteristics of species themselves such as their abundance. iv ACKNOWLEDGMENTS I would like to thank my parents, family and friends for their support and love over the long, long path to this dissertation. I would particularly like to thank my dad, mum, sister, Caitlin Kelly, Christine Avena, Brian Putnam, Kim Schoonover, Melinda Markin, Kevin Bracy Knight, Amber Churchill, Helen McCreery, Amanda Hund, Tim Szewczyk, Sierra Love Stowell, Julie Allen, Daisie Huang and Denise Tan. Aspects of my PhD relied on the assistance, mentorship, advice and on conversations with Hilmar Lapp, Nico Franz, Trish Rose-Sandler, William Ulate, Matt Yoder, Andrea Thomer, Dimitris Kontokostas, Dean Pentcheff, John Wieczorek and Walter Jetz. I would particularly like to thank Pat Kociolek, Erin Tripp, Andrew Martin, Andrew M. Johnson, Nico Cellinese and Hilmar Lapp for their patience, advice and support. As a PhD student, I have had many, many opportunities to work on fantastic projects unrelated to my core dissertation topic. I would like to thank the Wikimedia Foundation, NESCent, the Biodiversity Heritage Library, the Google Summer of Code project, and MCN for these opportunities. I am grateful to Nolan Kane and John M. Basey for the opportunity to teach undergraduate labs under their supervision. I would like to especially mention the developers of Java’s Stream API, without which this dissertation would have taken much longer. For Chapter 2. The tempo and mode of the taxonomic correction process in North American Birds over the last 127 years : Victoria Tersigni helped collect species description dates for this paper. I would like to thank Carla Cicero, Nico v Franz and John Bates for their feedback and comments on previous drafts of this manuscript and for Maxwell Joseph’s comments on the hierarchical model. My initial work on this project was funded by a graduate fellowship at the National Evolutionary Synthesis Center under the supervision of Hilmar Lapp. Most importantly: this dissertation could not have been begun, let alone seen to completion, without the advice, encouragement, feedback, criticism, inspiration and support of my Ph.D. advisor, Robert Guralnick. Thank you so much for everything, Rob. vi CONTENTS CHAPTER 1. INTRODUCTION ............................................................................................. 1 CHAPTER 2. THE TEMPO AND MODE OF THE TAXONOMIC CORRECTION PROCESS IN NORTH AMERICAN BIRDS OVER THE LAST 127 YEARS .............................................................. 9 Abstract ...................................................................................................................... 9 Introduction .............................................................................................................. 10 The importance of taxonomic checklists .............................................................. 13 Key questions ........................................................................................................ 16 Materials and Methods ............................................................................................ 17 Source data ........................................................................................................... 17 Taxonomic corrections .......................................................................................... 20 Differences in correction rates among higher-level taxa .................................... 21 Results ...................................................................................................................... 23 Overall trends in lumping and splitting .............................................................. 23 Full and partial reversions ................................................................................... 25 Corrections involving currently recognized species ............................................ 26 Which species are most likely to be lumped or split? .......................................... 28 Discussion ................................................................................................................. 29 Supplementary Materials ........................................................................................ 36 CHAPTER 3. THE COMPONENTS OF THE TAXONOMIC DISCOVERY PROCESS AND THE EFFECT OF ABUNDANCE IN THE ONGOING DISCOVERY OF NORTH AMERICAN FRESHWATER ALGAE ........................................................................................................................ 39 Introduction .............................................................................................................. 39 Methods .................................................................................................................... 48 Results ...................................................................................................................... 55 Changes in the Algal Checklists .......................................................................... 55 Measuring similarity between checklists ............................................................ 56 vii The cadence of taxonomic discovery .................................................................... 58 The effect of genus size on reorganization ........................................................... 64 The effect of abundance on lumping and splitting rates ..................................... 66 The effect of taxonomic uncertainty on interpretation of biodiversity data ...... 67 Discussion ................................................................................................................. 68 Stability of taxonomic checklists .......................................................................... 68 Individual taxonomic changes .............................................................................. 69 Insights into the process of taxonomy ................................................................. 73 Conclusion ............................................................................................................. 78 Supplementary Materials
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