Natural History Collections in the Science of the 21st Century

Roseli Pellens is a researcher in macroecology and systematics for conservation at the Institute of Systematics, Evolution and Biodiversity, France. Her research interests include openness and sharing in science, and the contribution of natural history collections as a sustainable source of data and inspiration.

• Foreword xviiBruno DAVIDAcknowledgments xxiRoseli PELLENSChapter 1 Natural History Collections: An Essential Resource for Science in the 21st Century 1Roseli PELLENS1.1 Collections in early 21st century science 21.2 New explorations because of the magnitude and diversity of the collections’ data 31.3 Research using and driving the constitution of natural history collections 51.3.1 Being able to return to the object: one of the major contributions of natural history collections 61.3.2 Collections at the heart of highly innovative research thanks to new technologies 71.3.3 A resource for global change research 81.3.4 Designing the science of the future based on collections 91.4 References 11Chapter 2 Natural History Collections: An Ancient Concept in a Present and Future Perspective 13Philippe GRANDCOLAS2.1 Introduction 142.2 A tribute to curiosity and coupling with classifications 142.3 The structuring of our thoughts and actions by an ancient concept 162.4 Collections: more than species catalogues 182.5 Big Data collections in space and time 192.6 What future is there for the use of collections? 202.7 Conclusion 222.8 References 22Chapter 3 Louis XIV’s Blue Gems: Exceptional Rediscoveries at the French National Museum of Natural History 27François FARGES3.1 Introduction 293.2 A scientific investigation of color 313.3 The digital decoding of the creative genius of the royal gem cutter 323.4 Epilogue: toward a renaissance 353.5 References 36Chapter 4. Rediscovering Human Mummies: Unpublished data on the Chachapoya Mummy Exhibited at the Musée de l’Homme 37Aline THOMAS, Arnaud ANSART, Christophe BOU, Jean-Bernard HUCHET, Véronique LABORDE, Samuel MERIGEAUD and Éloïse QUETEL4.1 Introduction 384.1.1 The Muséum’s collection of human mummies 384.1.2 Origin, discovery, donation and exhibition: a brief history of the mummy 404.2 Materials and methods 434.2.1 The MNHN-HA-30187 mummy: position of the body, measurements and external appearance 434.2.2 Medical imaging protocol and technique 454.2.3 Protocol for experimental reproduction of trepanation 454.3 Results 464.3.1 Basic biological identity 464.3.2 Osteo-dental status 474.3.3 Internal organs 484.3.4 Archeoentomology 504.3.5 Cranial trepanation: location, size and mode of operation 524.4 Discussion 544.4.1 Identity of the deceased and health status 544.4.2 Treatment of the corpse and embalming 554.4.3 Chronology of mortuary gestures 564.5 Conclusion 584.6 References 59Chapter 5 Reconstructing the History of Human Populations: A Challenge for Biological Anthropology 63Martin FRIESS and Manon GALLAND5.1 Introduction 635.1.1 How human remains have also become scientific objects 635.1.2 The MNHN biological anthropology collection 645.1.3 Cranial morphology as an indication of biocultural processes 655.2 Cranial morphology and settlement history 665.2.1 A new look at the diversity of Native Americans 695.3 Cranial morphology and adaptation to the environment 715.3.1 Cranial diversity beyond randomness 735.4 The importance of cranial collection for the advancement of research in biological anthropology 755.5 References 76Chapter 6 The Discovery of New Metal-Hyperaccumulating Plant Species in Herbaria 79Vanessa R. INVERNÓN, Romane TISSERAND, Pierre JOUANNAIS, Dulce M. NAVARRETE GUTIÉRREZ, Serge MULLER, Yohan PILLON, Guillaume ECHEVARRIA and Sylvain MERLOT6.1 Metal-hyperaccumulating plants 806.2 The screening of herbarium collections: from atomic absorption to X-ray fluorescence 836.3 The discovery of new metal-hyperaccumulating plants at the MNHN herbarium 856.3.1 The interest of the MNHN herbarium for the research of metal-hyperaccumulating plants 856.3.2 From the herbarium to the field: new nickel hyperaccumulators in the genus Orthion 876.3.3 Rinorea multivenosa, the first zinc hyperaccumulating species discovered in the Amazon basin 886.3.4 A large number of manganese hyperaccumulating species to be discovered 906.4 Conclusion 916.5 Acknowledgments 926.6 References 92Chapter 7 Fossil Crustaceans in the Light of New Technologies 95Sylvain CHARBONNIER and Marie-Béatrice FOREL7.1 Introduction 967.2 Fossil crustaceans 967.3 The radiation of fossil crustaceans 987.3.1 Revealing characters with UV light (yellow fluorescence) 987.3.2 Revealing characters with green light (green–orange fluorescence) 997.3.3 X-ray radiography 1007.4 Exceptional preservation of fossil crustaceans 1027.5 Ostracods and paleogeography at the end of the Paleozoic 1057.6 References 105Chapter 8 The “Cyanobacteria and Microalgae” Collection in the Time of “-omics” 109Sébastien DUPERRON, Charlotte DUVAL, Sahima HAMLAOUI, Katia COMTE, Claude YÉPRÉMIAN and Cécile BERNARD8.1 Introduction 1098.2 A living collection supported by research 1118.3 New uses of the collection in basic research 1148.3.1 Polyphasic identification and taxonomy of cyanobacteria and microalgae 1148.3.2 Contribution to the evolutionary sciences 1148.3.3 Contribution to the study of interactions between organisms 1158.4 Enhancing the value of biological resources through the search for innovative bioactive molecules 1168.5 Expertise in environmental diagnosis 1188.6 The living collection of cyanobacteria and microalgae of today and tomorrow 1198.7 References 121Chapter 9 The Collection of Cryopreserved Cells and Tissues of Vertebrates: Methods and Application 125Michèle GERBAULT-SEUREAU and Bernard DUTRILLAUX9.1 Introduction 1269.2 History of the collection 1269.3 Can all living beings be cryopreserved? 1279.3.1 Collection, culture and freezing 1289.4 Current applications 1309.5 Current composition of the bank 1339.6 Perspectives 1369.7 References 137Chapter 10 Herbaria, the Last Resort for Extinct Plant Species 139Serge MULLER, Valérie PRIOLET, Éric BADEL and Stéphane BUORD10.1 Context and objectives 14010.2 Proposed approach and protocol 14110.3 First results 14210.3.1. Selection of target species and identification of affine species 14210.3.2 Assessment of the viability of available seeds 14510.3.3. Cultivation experiments on affine species of the target species 14910.4 Discussion and conclusion 15210.5 Acknowledgments 15410.6 References 154Chapter 11 Ocean Cores, Climate Archives 159Eva MORENO and Annachiara BARTOLINI11.1 Introduction 16011.2 The MNHN’s oceanic collection 16011.3 Development of core drilling techniques 16111.4 Ocean cores: archives of past climate variability 16311.5 Climate proxies 16411.5.1 Temperature proxies 16511.5.2 Proxies of salinity 16911.5.3 Paleo-pH proxies and carbonate ion concentration 17011.6 Analytical techniques 17111.7 Conclusion 17211.8 References 173Chapter 12 Clarifying the Radiocarbon Calibration Curve for Ancient Egypt: The Wager of Herbaria 177Anita QUILES, Vanessa R. INVERNÓN, Lucile BECK, Emmanuelle DELQUE-KOLIC, Myriam GAUDEUL, Serge MULLER and Germinal ROUHAN12.1 Introduction 17812.2 Carbon-14 (14 C) dating and Egyptian chronology 17912.2.1 The challenge of calibration 17912.2.2 Chronology of ancient Egypt: contribution of 14 C and historic debates 18112.3 Specificities of the Egyptian landscape and the objective of the project 18212.4 The flora of Egypt in the MNHN Herbarium 18412.5 Analytical and statistical challenges 18612.5.1 Selection of herbarium specimens 18712.5.2 Preliminary results of 14 C dating 18712.6 Conclusion 19012.7 References 191Chapter 13 Herbaria, a Window into the Evolutionary History of Crop Pathogens 195Lionel GAGNEVIN, Adrien RIEUX, Jean-Michel LETT, Philippe ROUMAGNAC, Boris SZUREK, Paola CAMPOS, Claudia BAIDER, Myriam GAUDEUL and Nathalie BECKER13.1 Epidemics, emergences and re-emergences 19613.2 Development of agriculture, domestication of cultivated plants and their diseases 19713.3 Molecular biology and genomics as a tool for studying phytopathogenic micro-organisms 19913.4 Contributions of the herbarium samples 19913.4.1 Direct evidence 20013.4.2 Molecular analyses 20113.5 How to explore a herbarium 20313.6 Characteristics of old nucleic acids and their treatment 20513.6.1 The particular case of viral nucleic acids 20613.7. Xanthomonas citri pv. citri and its emergence in the Indian Ocean 20813.8 Emergence and evolutionary history of plant pathogenic viruses: the geminivirus model 20913.8.1 Case of a species complex responsible for an emerging disease 21013.8.2 Case of a cryptic geminivirus 21113.9 Discussion 21213.10 Acknowledgments and funding 21313.11 References 213Chapter 14 The Yellow-Legged Asian Hornet: Prediction of the Risk of Invasion and the Study of its Color Variations 219Claire VILLEMANT, Quentin ROME and Adrien PERRARD14.1 Introduction 22014.2 Vespa velutina: some elements of taxonomy and biology 22214.2.1 A species: 13 colored forms 22214.2.2 One nest per year 22314.2.3 Insectivore, but not exclusively 22314.3 Sampling of specimens 22414.4. The origin of invasive lineages of V. velutina in France and Korea 22514.4.1 The history of the invasion explained by genetics 22514.4.2. A single queen at the origin of the invasive lineage in France .. 22614.5 Expansion risks in Europe and worldwide 22614.5.1 Data and methods for inferring range and predicting invasion risk 22614.5.2 Strong expansion in Europe and the Northern Hemisphere 22714.6 Origin of color and shape variations 22914.6.1 The importance of collection specimens 22914.6.2 Discordance between genetic lineages and colored forms 23114.7 Conclusion 23214.8 References 233Chapter 15 Exploring Temporal Changes in the Composition of Macroalgal Communities by Using Collections 235Marine ROBUCHON, Éric FEUNTEUN, Romain JULLIARD, Florence ROUSSEAU and Line Le GALL15.1 On the constitution of macroalgal collections 23615.1.1 Large seaweeds 23615.1.2 Algal herbaria 23615.1.3 Data associated with the herbaria 23715.1.4 Specimens and scientific evidence 23715.1.5 The herbarium of the Dinard maritime laboratory 23915.2 Exploring temporal changes in species distribution 23915.2.1 Perspectives for exploring temporal changes in species distribution 24515.3 Exploring temporal changes in community composition 24615.3.1 Example of the study of the Dinard Herbarium 24615.3.2 Perspectives for exploring temporal changes in community composition 24715.4 Conclusion: sampling and analysis strategies for the future 24815.5 References 249Chapter 16 Herbaria, Witnesses of the Stakes of Biodiversity Conservation and the Impacts of Global Changes 251Serge MULLER, Vanessa R. INVERNÓN and Germinal ROUHAN16.1 Introduction 25216.2 Evaluation of the floristic richness and conservation issues of territories 25416.3 Studies of introduction pathways and colonization of invasive exotic plants and pathogens 25716.4 Analysis of the impact of pollution and changes in air quality 25916.5 Study of phenological changes in flora as a result of climate change 26016.6 Conclusion 26216.7 References 263Chapter 17 Digital Photography In Natura in Zoology: More Biology in Natural History Collections? 271Romain GARROUSTE17.1 Images and collections for comparative biology 27217.2 Accelerating the process of the incomplete inventory of life 27417.3 Why more biology in natural history collections? 27717.4 Images in the natural sciences: a collection like any other? 28017.5 The Hemiptera of France: an exemplary iconography 28217.6 Trait databases, query automation and bio-inspiration 28217.7 Conclusion: a new challenge for natural history 28417.8 References 285Chapter 18 The Use of Large Natural History Datasets to Respond to Current Scientific and Societal Issues 289Anne-Christine MONNET, Thomas HAEVERMANS, Anne-Sophie ARCHAMBEAU, Philippe GRANDCOLAS and Roseli PELLENS18.1 Introduction 28918.2 Making data available: a revolution 29018.3 Challenges for data providers 29318.3.1 Reading labels or directories 29318.3.2 Structure of the information related to the specimens 29418.3.3 The taxonomic framework: moving information 29518.3.4 The importance of tracing the source of data 29618.4 The role of access portals 29618.4.1 The provision standards 29718.5 The importance of scientific analysis design in appropriating the specificities of data from collections 29918.5.1 Detecting the biases in collection data: advantages and opportunities for scientific analyses 29918.5.2 Toward a good balance between the question and the available data 30018.5.3 Playing the advantage of multiple spatial scales 30118.6 Moving from raw data to sorted data that can be used for scientific analyses 30118.6.1 From open data to open science, a responsibility for the traceability of data and operations 30318.6.2 Toward a necessary reorganization of collaborative work 30418.7 Conclusion 30618.8 References 307Chapter 19 Is There a Need for Biocultural Collections? State of the Art and Perspectives 311Serge BAHUCHET19.1 Introduction 31119.2 Origin of these collections 31219.2.1 Ethnobotany 31219.2.2 Ethnology 31319.3 Collection principles and the function of collections 31319.3.1 The role of objects in “Maussian” ethnology 31319.3.2 Ethnobotanical collections 31519.3.3 Biocultural collections 31719.4 Principles for the articulation of sets 31919.5 Description of the collections 32419.5.1 Ethnobiological specimens 32519.5.2 Objects and artifacts 32919.6 What changes? 33219.7 References 334Chapter 20 Why Preserve? 337Véronique ROUCHON20.1 The museum’s collections: between study and heritage 33820.2 Disrupting the equilibrium 33920.3 Preparation and storage 34220.4 The main principles of conservation 34620.5 The main principles of conservation being undermined 34720.6 Multiple values 34920.7 The scientific value of the collections 35120.8 Conclusion 35720.9 References 357Chapter 21. Collections for Scientific Research in the 21st Century and Beyond 359Roseli PELLENS21.1 Collections in the quest for knowledge 35921.2 Three main kinds of new uses for collections 36021.2.1 Enriching the life sciences, human sciences and the sciences of the universe with new technologies 36021.2.2 A pool of information on the environment 36021.2.3 The era of digital data 36221.3 Lessons from these new uses 36221.3.1 The importance of richness and diversity 36321.3.2 Information at the heart of new research 36321.3.3 Good conservation and good practices 36521.3.4 The importance of sets 36621.4 Collections in 21st century science and beyond 36721.5 Conclusion 36721.6 References 369List of Authors 373Index 381