The Extended Specimen: Emerging Frontiers in Collections-Based Ornithological Research (Studies in Avian Biology)

__The Extended Specimen__ highlights the research potential for ornithological specimens, and is meant to encourage ornithologists poised to initiate a renaissance in collections-based ornithological research. Contributors illustrate how collections and specimens are used in novel ways by adopting emerging new technologies and analytical techniques. Case studies use museum specimens and emerging and non-traditional types of specimens, which are developing new methods for making biological collections more accessible and "usable" for ornithological researchers. Thus, book documents the power of ornithological collections to address key research questions of global importance. Cover 1 Half Title 2 Title Page 4 Copyright Page 5 Table of Contents 6 Contributors 8 Preface 12 Chapter 1: The Extended Specimen 14 Extending the Traditional Specimen 17 Extending the Specimen Concept 17 Conclusion: Just What Is the “Extended Specimen?” 19 Acknowledgments 20 Literature Cited 20 Chapter 2: Getting under the Skin 24 Avian Anatomical and Skeletal Collections 25 Comparative Anatomy 26 Systematics of Extant Species 27 Morphology and Behavior 28 Paleontology 28 Morphometrics 29 Physiology and Functional Anatomy 31 Evolution and Development 31 Conclusions and Future Directions 31 Acknowledgments 32 Literature Cited 32 Chapter 3: Advanced Methods for Studying Pigments and Coloration Using Avian Specimens 36 Spectrophotometry 37 Limitations and Considerations for Using Specimens 38 Analytical Approaches 38 Applications to Ecology and Evolution 41 Future Directions 42 Digital Photography and Hyperspectral Imaging 42 Chromatographic Analyses of Bird Pigments 43 Analytical Approaches 43 Benefits and Challenges of Using Specimens 46 Future Directions 47 Nondestructive Analysis with Raman Spectroscopy 47 What Is Raman Spectroscopy? 47 Comparing Raman Spectroscopy and Spectrophotometry 48 An Overview of Raman Spectroscopy and Plumage Pigments 49 Applications of Raman Spectroscopy in Museum Collections 50 Advances in Studying Structural Coloration 50 Mechanisms of Structural Coloration 51 Techniques to Describe Structural Coloration 51 Applications to Ecology and Evolutionary Biology 52 Structural Coloration in Fossil Feathers 52 Future Directions 52 Advanced Methods for Studying Avian Egg Color 53 Egg Coloration: An Overview 53 Chemical Analysis 54 Structural Analysis 55 Spectrophotometry 55 Digital Photography 56 Case Study 56 Future Directions 58 Conclusions 58 Literature Cited 58 Chapter 4: Integrating Museum and Media Collections to Study Vocal Ecology and Evolution 70 Species Limits and Geographic Variation in Bird Song 72 Cultural Evolution and Temporal Variation in Avian Vocal Displays 73 Behavioral Responses to Geographic and Temporal Variation in Song 74 Macroevolutionary Patterns of Avian Vocalizations 75 Linking Museum Vouchers and Audio Recordings 79 Parallel Advances in Nonavian Taxa 81 Conclusions and Future Directions 82 Acknowledgments 82 Literature Cited 82 Chapter 5: Leveraging Diverse Specimen Types to Integrate Behavior and Morphology 88 Insights into the Origin of Novelty in the Manakins (Pipridae) 89 Manakin Methods 89 Physical Specimens 91 Digital Media Specimens 91 Meta-Analyses 92 Functional Morphology 92 Evolutionary Analyses 92 Manakin Results 92 How It Works: The Functional Morphology of the Club-winged Manakin Sonation 92 How It Evolved: The Integrated Evolutionary Patterns of Character Change 93 The Courtship Phenotype of the Bird-of-Paradise (Paradisaeidae) 95 Birds-of-Paradise: A Modeling Approach 95 General Conclusions 98 Acknowledgments 100 Literature Cited 100 Chapter 6: Emerging Techniques for Isotope Studies of Avian Ecology 102 Stable Isotopes: Basic Theory and Methodology 104 Avian Specimens in Stable Isotope Ecology 105 Emerging Analytical Techniques 108 Potential Confounding Factors and Other Sources of Error 109 Strategies for Sampling Museum Specimens 111 Challenges and Recommendations for Future Museum Collections and Isotope Studies 115 Conclusions 116 Acknowledgments 116 Literature Cited 116 Chapter 7: What Bird Specimens Can Reveal about Species-Level Distributional Ecology 124 Joseph Grinnell: A Central Figure in Distributional Ecology 126 The Grinnell Project 126 Present-Day Studies in Distributional Ecology 127 What Can Be Learned? 129 Dynamics of Ecological Niches through Time 129 Dynamics of Distributional Areas through Time 130 Links among Niche, Geography, and Population Biology 132 What Comes Next? 132 Acknowledgments 133 Literature Cited 133 Chapter 8: Using Museum Specimens to Study Flight and Dispersal 140 Morphological Traits and Flight 141 Methods for Estimating Flight Performance from Specimens 142 Estimating Flight Performance from Traditional Study Skins 142 Hand-Wing Indices 142 Wing Area Indices 144 Estimating Flight Performance from Extended Specimens 145 Preparation of Specimens Useful for Aerodynamic Calculations 145 Estimation of Total Wing Area 147 Aspect Ratio 148 Lift-to-Drag Ratio 148 Flight Muscles and Hearts 150 The Use of Museum Specimens to Assess Flight Performance and Its Ecological and Evolutionary Consequences 151 Diversification Rates 151 Genome Size Evolution 151 Future Directions 152 Acknowledgments 152 Literature Cited 152 Chapter 9: Transforming Museum Specimens into Genomic Resources 156 Background: First Forays into the Genomes of Museum Specimens 157 The Game-Changer: Next-Generation Sequencing 158 Choosing a Next-Generation Sequencing Technique 158 Problems with Sequence Data Specific to Ancient DNA 161 Case Studies in Ornithology 162 Future Directions 163 Returning to Fundamentals: DNA Extraction 163 Archiving Data: One Researcher’s Trash Is Another’s Treasure 164 Analytical Programs for Detecting DNA Damage and Contamination 164 Conclusions 164 Acknowledgments 165 Literature Cited 165 Chapter 10: Methods for Specimen-based Studies of Avian Symbionts 170 Before You Begin: The Field Notebook 174 Sampling Protocols for the Study of Blood Parasites (Haematozoa) 175 Blood Collection and Storage 176 Preparation and Fixation of Blood Smears 177 Sampling Protocols for the Study of Microbial Symbionts (Bacteria, Fungi, and Viruses) 179 Sampling Protocols for the Study of Ectoparasites 181 Fumigation and Collection of Ectoparasites 181 Preparation and Curation of Ectoparasite Specimens 183 Sampling Protocols for the Study of Endoparasites 184 Examination of Gastrointestinal Tract and Other Organs for Endoparasites 184 Fixation of Helminths 187 Preparing Endoparasites for Morphological Study 190 Conclusion 192 Acknowledgments 193 Literature Cited 193 Chapter 11: Student-Led Expeditions as an Educational and Collections-Building Enterprise 198 Expanding the Scope of Natural History Museums 198 The Complete Specimen Package 200 Cornell Expeditions in Field Ornithology and Ivy Expeditions 201 General Themes and Ongoing Activities of the Expeditions Program 203 Setting the Framework 203 Responsibilities of the Students 204 Responsibilities of the Advisers 204 Specimens, Their Curation, and Important Logistics 205 Data Curation 206 Experiences in Pre-expedition Work 206 Seminar 206 Picking Field Sites and Seasons 207 Proficiency in Field Skills 207 Health and Risk Management 207 Managing Travel and the Budget 208 Experiences during the Expeditions 208 Time Management and Good Habits in the Field 208 Collecting the Complete Specimen Package and Other Natural History Data 209 Outreach 209 Experiences in Post-expedition Work 209 Outcomes: Specimens and Papers 209 Conclusions 210 Acknowledgments 212 Literature Cited 212 Chapter 12: Biodiversity Informatics and Data Quality on a Global Scale 214 Data Sources, Standards, and Sharing 215 Birds in the Cloud: Increasing Data Access through VertNet 216 Data Quality: Fallacies and Truth 221 Data Perfection 222 Data Petrification 222 Data Fitness for Use 222 Biodiversity Data and Emerging Research 224 Niche Evolution and Speciation 224 Risk Assessment of Invasive Species 225 Phenotypic Evolution and the Colonization of Novel Habitats 225 Latitudinal Gradients and Evolutionary Divergence 226 Biodiversity and Conservation Planning 226 Conclusions and Future Needs 227 Acknowledgments 228 Literature Cited 228 Chapter 13: Ornithological Collections in the 21st Century 232 The Once and Future Specimen 234 Blurring the Lines between “Specimen” and “Data” 235 The Accessibility Challenge 237 The Evolving Collecting Expedition 239 Conclusions: Back to the Future 240 Acknowledgments 241 Literature Cited 241 Index 246 STUDIES IN AVIAN BIOLOGY 252 The Extended Specimen highlights the research potential for ornithological specimens, and is meant to encourage ornithologists poised to initiate a renaissance in collections-based ornithological research. Contributors illustrate how collections and specimens are used in novel ways by adopting emerging new technologies and analytical techniques. Case studies use museum specimens and emerging and non-traditional types of specimens, which are developing new methods for making biological collections more accessible and "usable" for ornithological researchers. Published in collaboration with and on behalf of The American Ornithological Society, this volume in the highly-regarded Studies in Avian Biology series documents the power of ornithological collections to address key research questions of global importance. "The Extended Specimen highlights the research potential for ornithological specimens, and is meant to encourage ornithologists poised to initiate a renaissance in collections-based ornithological research. Contributors illustrate how collections and specimens are used in novel ways by adopting emerging new technologies and analytical techniques. Case studies use museum specimens and emerging and non-traditional types of specimens, which are developing new methods for making biological collections more accessible and "usable" for ornithological researchers. Thus, book documents the power of ornithological collections to address key research questions of global importance."--Provided by publisher This book highlights the research potential for ornithological specimens, and stimulates ornithologists poised to initiate a renaissance in collections-based ornithological research. Contributors illustrate collections and specimens in novel ways by adopting emerging new technologies and analytical techniques. Case studies display the use of museum specimens, emerging and non-traditional types of specimens, and developing new methods for making biological collections more accessible and "usable" for ornithological researchers. The book demonstrates the power of ornithological collections to address key research questions at global scales. "The author has achieved the breakthrough of generalizing the First-Order Theory presented in his previous books, to the efficient computations of arbitrarily high-order sensitivities for nonlinear systems (HONASAP). This breakthrough has many applications, especially when there is a need to quantify nonlinear behavior or to quantify uncertainties in design parameter/system responses in large-scale systems. This book presents the theory of the HONASAP with applications, from simple, analytically solvable, paradigm problems to large-scale applications in thermal hydraulics, particle transport, etc."--Provided by publisher The book demonstrates the power of ornithological collections to address key research questions at global scales through emerging new technologies, analytical techniques, and case studies. The book includes developing methods for making biological collections more accessible and "usable" for ornithological researchers.