View Can Be a Dangerous Luxury When Substituted for Insight and Understanding
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Fairyland is nothing but the sunny country of common sense. -- G.K. Chesterton In fact, we were probably wrong about everything, and, no doubt, still are. Whenever we come to a conclusion, we should just assume we’re wrong and go from there. -- Steven Brust, P.J.F. A point of view can be a dangerous luxury when substituted for insight and understanding. -- Marshall McLuhan Since no one is perfect, it follows that all great deeds have been accomplished out of imperfection. Yet they were accomplished, somehow, all the same. -- Lois McMaster Bujold The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka!” but “That’s funny…” -- Isaac Asimov The interplay of ideas and the oblique uses of knowledge are often of extraordinary interest. --Sir Arthur Conan Doyle In every object there is inexhaustible meaning; the eye sees in it what the eye brings means of seeing. -- Goethe If all else fails, look at the plant. -- Gar W. Rothwell I don’t necessarily believe everything I say. -- Marshall McLuhan University of Alberta Fossil Taxa in the Family Pinaceae, and their Phylogenetic Implications by Ashley Annette Klymiuk A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Master of Science in Systematics & Evolution Department of Biological Sciences © Ashley A Klymiuk Fall 2011 Edmonton, Alberta Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission. DEDICATION To Fluffy. ABSTRACT Although the peak diversity of Pinaceae is reflected by many Cretaceous seed cones representing extinct genera, the oldest definitive record of the family is attributable to an extant genus. A seed cone discovered at the Valanginian Apple Bay locality extends the record of Picea by ~75 Ma, resolving a ghost lineage predicted by molecular dating analyses. However, a pine from the Eocene Princeton Chert indicates that extant genera are themselves relicts of greater historical diversity. Pinus arnoldii Miller is reconstructed here as the first organismal concept for an extinct member of Pinaceae, on the basis of anatomical attachments between the seed cones attributable to Subgenus Pinus, and vegetation like that of Subgenus Strobus. The phylogenetic implications of these fossils are assessed through cladistic analyses, and comparisons with maximum likelihood ancestral states reconstructed on topologies derived from Bayesian cpDNA analysis of extant Pinus and Picea. ACKNOWLEDGEMENTS I am indebted first and foremost to my supervisor, Professor Emeritus Ruth A. Stockey, for support, advice, and helpful discourse over the preceding half-decade. Dr Stockey took a chance on hiring the geeky kid with the laptop, and I appreciate it more than mere words can express. She gave me a step up into the fascinating world of research science, and challenged me to exceed my highest expectations -- I’ve no doubt that I’ve become a better researcher and scholar under her tutelage. My co-supervisor, Dr. Jocelyn Hall, also deserves recognition for stepping in at the ninth hour to undertake the daunting task of, principally, calming me down, but no less importantly, teaching me the language of molecular systematics -- my own inadequacies may produce grammatical errors, but I’d be thoroughly lost without the vocabulary she instilled. Dr. Randy Currah kept tabs on me during my supervisor’s sabbatical in 2009-2010, and I’m grateful for the caffeine and conversation. Dr. Genaro Hernandez-Castillo similarly merits gratitude for caffeine and conversation – I generally rank these equally (and highly), but there’s no doubt in my mind that conversation proved more beneficial to my development as a scientist. Dr. Gar Rothwell (Distinguished Professor, Ohio University, Athens) was an invaluable mentor and advocate, and I should like to think that I’ve internalized at least of few of his varied maxims on science. As is indubitably apparent, I’ve not suffered in the least for lack of scientific models upon which to pattern myself, and all are deserving of my gratitude. I hope only that I can prove to have been deserving of their time. I also owe a great debt to Dr. Stacey Gibb, who told me that she thought I was smart when I most desperately needed to hear it. Drs Jocelyn Hall (Department of Biological Sciences), Randy Currah (Biological Sciences), and Alex Wolfe (Department of Earth & Atmospheric Sciences) agreed to serve on my committee, for which I am exceedingly grateful. Botany, let alone my own humble research, owes a debt to Charles N. Miller, Jr., who made detailed anatomical studies of living and fossil conifers. These materials, collectively known as the University of Montana Conifer Reference Collection, were selflessly donated to RA Stockey, and have proved an invaluable resource for numerous studies. Thanks are also owed to David Gernandt (UNAM), Aaron Liston and Matthew Parks (OSU Corvallis) for provision of Pinus sequence data, and to CS Campbell (UMaine) and his colleagues for access to unpublished Picea sequence data. The Willi Hennig Society has unknowingly supported my research, by ensuring the phylogenetic analysis program TNT is made publicly available (www.cladistics.com). Thanks are also owed to Kevin C. Nixon (Cornell) -- I have been a beneficiary of the Asado (v1.1 beta) program that he designed. My research was financially supported in part by Natural Sciences and Engineering Research Council of Canada Discovery Award A-6908 to RAS, and National Science Foundation grant EF-0629819 to GWR and RAS. The Department of Biological Sciences, University of Alberta, provided financial support in the form of a graduate teaching assistantship. My gratitude to the Department extends beyond these thanks, however: teaching undergraduate botany courses allowed me a rare window within which to organize some of my own thoughts about my discipline, and about scientific methodology. Following in that vein, I would like to further extend my thanks to the numerous students I have had the privilege to engage with, including the summer students who not only enlivened life in the lab over the past few years (Slacker Fridays and sudoku were never so much fun as in those halcyon summer days), but more importantly Accomplished An Awful Lot of Nasty Tasks. Finally, sincere appreciation is most definitely owed to my mother, who puts up with more whining than any human being should reasonably have to. Thanks, Mum. TABLE OF CONTENTS CHAPTER I Introduction to the Natural History and Phylogeny of the Family Pinaceae 1 Literature Cited 14 CHAPTER II A Lower Cretaceous Picea-like Seed Cone From Vancouver Island 23 Introduction 23 Material and Methods 25 Geologic and Depositional Setting 25 Specimen Preparation 28 Phylogenetic Analyses 29 Results 32 Systematics 32 Description 33 Phylogenetic Analysis 36 Discussion 38 Literature Cited 51 CHAPTER III: The First Organismal Concept for an Extinct Species of Pinaceae: Pinus arnoldii Miller 74 Introduction 74 Material and Methods 77 Results 79 Systematics 79 Amplified Diagnosis 79 Description 82 Phylogenetic Analysis 93 Full Plastome Sequences 94 rbcL and matK Sequences 95 Discussion 97 Whole Plant Reconstruction 97 Phylogeny 102 Literature Cited 107 CHAPTER IV Inductive Approach to Fossil Taxonomy Using Maximum Likely Ancestral State Reconstruction 133 Introduction 133 Materials and Methods 139 cpDNA 139 Morphology 140 Phylogenetic Analyses 141 Results 143 Morphological Analyses 143 cpDNA Analyses for Picea 143 cpDNA Analyses for Pinus 145 Ancestral State Reconstruction 146 Discussion 147 Concordance of tree topologies with previous studies 147 Implications for further research 151 Literature Cited 154 CHAPTER V Evolutionary Context and Phylogenetic Applications of Newly-Described Pinaceous Taxa 179 Early Cretaceous Record for Picea 183 Pinus arnoldii Miller, an Organismal Concept 186 Applications of these Taxa in Molecular Systematics 192 Further Research 197 Literature Cited 199 APPENDICES Appendix A: Concepts of characters for pinaceous seed cones 213 Appendix B: Morphological character scorings for Pinus 218 Appendix C: Concepts of characters scored for Pinus 221 Appendix D: Morphological character scorings for Picea 225 LIST OF TABLES Table 3-1. Morphological matrix for pinaceous seed cones and their stratigraphic context 63 LIST OF FIGURES Fig. 2-1 66 Picea burtonii sp. nov. Holotype UAPC-ALTA P16098. Fig. 2-2 68 Picea burtonii sp. nov. Holotype UAPC-ALTA P16098. Fig. 2-3 70 Picea burtonii sp. nov. Holotype UAPC-ALTA P16098. Fig. 2-4 71 Origin and architecture of lateral resin canal and vascular systems within base of bract- scale complexes. Fig. 2-5 73 Nelson consensus trees produced from analysis of 33 morphological characters using the parsimony ratchet perturbation algorithm (Nixon 1999). Fig. 3-1 114 Pinus arnoldii seed cones (UAPC-ALTA). Fig. 3-2 116 Pinus arnoldii seed cones (UAPC-ALTA) and P. mugo branches. Fig. 3-3 118 Ovules of Pinus arnoldii (A, B; UAPC-ALTA) and extant Pinus mugo (C, D) at pollination stage. Fig. 3-4 120 Pinus arnoldii seed cone attachments, stems, and wood (UAPC-ALTA). Fig. 3-5 122 Pinus arnoldii short shoots and leaves (UAPC-ALTA). Fig. 3-6 124 Pinus arnoldii pollen cones and pollen (UAPC-ALTA). Fig. 3-7 126 Pinus arnoldii roots and ectomycorrhizal associations (UAPC-ALTA). Fig. 3-8 128 Single most-parsimonious tree produced from a combined matrix of full plastome sequences (Parks et al.