Inventory of Biodiversity Today

Violaine Nicolas is Professor at the Muséum national d'histoire naturelle in Paris, France, and Director of the Institut de systématique, évolution, biodiversité, France.

• Introduction xiiiViolaine NICOLASChapter 1. Scientific Exploration Campaigns to Inventory Existing Biodiversity and Hasten the Discovery of New Species 1Line LE GALL1.1. Introduction 11.2. A historical overview of diversity inventory 21.3. The advent of molecular taxonomy 31.4. Biodiversity: the emergence of a concept in the face of the crisis 41.5. An incomplete inventory of diversity 51.6. The place of scientific exploration campaigns, run by the French Natural History Museum, in the inventory of biodiversity 61.7. Innovations to speed up the description of species 71.8. Challenges and issues surrounding scientific exploration campaigns 81.9. Conclusion 91.10. References 9Chapter 2. Half a Century of Naturalist Exploration of Upper Bathyal Benthic Environments: Ruptures and Continuities 11Sarah SAMADI and Sophie BARY2.1. The deep ocean: we have barely begun to plumb the depths 112.2. The Tropical Deep-Sea Benthos program 122.2.1. From MUSORSTOM to Tropical Deep-Sea Benthos 122.2.2. TDSB campaigns across time and space 132.2.3. Program metrics 192.3. Continuity and ruptures in the TDSB program 192.3.1. The place of "living fossils" in discourse on the deep oceans 192.3.2. A program evolving with societal issues 212.4. Campaigns at sea with taxonomic results: a network dynamic around naturalist collections 222.5. References 23Chapter 3. CEAMARC: An Integrated Campaign to Evaluate Biodiversity at All Scales in Adélie Land 27Marc ELÉAUME, Nadia AMÉZIANE, Frédéric BUSSON, Romain CAUSSE, Agnès DETTAÏ, Guillaume LECOINTRE and Catherine OZOUF-COSTAZ3.1. Introduction 273.2. The CEAMARC expedition (Collaborative East-Antarctic Marine Census) 293.2.1. An "integrated" campaign 293.2.2. Sampling methods 313.3. Some results 343.4. Conclusion 363.5. References 37Chapter 4. Objectif Plancton: A Citizen Science Program to Study Plankton Diversity 41Cyril GALLUT, Céline LIRET, Marine LE MOAL, Philippe PONDAVEN, Cécile BANOVSKI-KLEIN, Mathilde CADIER, Antoine CHARPENTIER, Klervi FUSTEC, Julianne LE GUEN, Molène LE ROY, Joëlle PICHON, Martin PLUS, Laura SCHWEIBOLD, Marc SOURISSEAU and Nalani K. SCHNELL4.1. A citizen science project 414.2. Scientific objectives 434.3. Materials and methodology 454.4. Avenues of research 494.4.1. Ichthyoplankton 494.4.2. Phytoplankton 514.4.3. Human and social sciences 534.5. Conclusion 554.6. References 56Chapter 5. Environmental DNA for Observing Marine Mammals in the Marine Protected Areas of Iroise and the Antilles 59Jean-Luc JUNG5.1. Introduction 595.2. Studying cetaceans in order to know them better: from visual observation to DNA analysis 615.3. Progress in approaches using environmental DNA (eDNA) and metabarcoding 625.4. Detection of marine mammals by eDNA analysis 635.5. First campaign in the Iroise Sea, 2019-2020 645.6. The An Bad’lo campaign in Martinique 665.7. Detection of marine mammals and other mobile marine fauna through the study of eDNA: from naturalist inventories to the support of public policies 685.8. References 69Chapter 6. DNA Barcoding for Identifying Species and Monitoring French Biodiversity 73Rodolphe ROUGERIE, Lucas SIRE and Antoine LÉVÊQUE6.1. Introduction 736.2. DNA barcoding for species identification 756.2.1. A simple and standardized tool for molecular identification 756.2.2. From the specimen to the community: identification by DNA barcoding and metabarcoding 766.2.3. DNA barcodes of the living world: a collective and international effort 796.3. DNA barcode libraries for biodiversity in Metropolitan France and overseas territories 816.4. Main challenges for the molecular identification of species in France 846.4.1. Development of exhaustive and accessible reference libraries 846.4.2. Molecular identification of species: an asset for monitoring French terrestrial biodiversity 866.5. Conclusion and perspectives 886.6. References 88Chapter 7. Exploring the Molecular Biodiversity of Specimens in Collections: The Case of Coccinellidae 95Karen SALAZAR, Romain NATTIER and Guillaume ACHAZ7.1. Introduction 957.2. DNA sequencing of collection specimens 967.3. Methodology for DNA sequencing of collection specimens 977.3.1. Extraction of DNA from collection specimens 977.3.2. Difficulties in the molecular use of collection specimens 977.3.3. Next-Generation Sequencing (NGS) technologies used in museomics 987.4. Recent results from museomic studies on insects 997.5. Context of the study on biodiversity and systematics of Coccinellidae 1067.5.1. Applications of museomics for exploring the biodiversity of Coccinellidae 1077.5.2. Barriers to the exploration of Coccinellidae biodiversity 1097.6. Conclusion 1127.7. References 112Chapter 8. New Tools and New Discoveries inPaleo-entomology: Looking to Future Challenges 123André NEL, Patricia NEL, Jean-Paul KUNDURA, Romain GARROUSTE, Valérie NGÔ-MULLER, Mathieu BODERAU, Thomas SCHUBNEL and Corentin JOUAULT8.1. Insects as essential players in past and present ecosystems 1238.2. Discovering the past to understand the present (and perhaps predict the future) 1258.2.1. A science which, until recently, had been largely overlooked 1268.2.2. Spectacular recent progress in data analysis 1278.3. Modern information-capture tools 1288.3.1. Bibliography: "I had a dream" 1288.3.2. The field 1298.3.3. Fossil preparation 1298.3.4. Information capture from fossils 1308.4. More "exotic" approaches 1318.4.1. Fossil trophic interactions 1318.4.2. DNA and organic chemistry 1328.5. Conclusion 1328.6. References 133Chapter 9. X-ray Tomography of Crinoids: Morphological Diversity and Evolution Seen under a Different Light 139Pablo MARTINEZ-SOARES, Nadia AMÉZIANE, Marta BELLATO, Julien BIGOT, Margot MATHIEU, Michel ROUX, Patricia WILLS and Marc ELÉAUME9.1. X-ray microtomography 1399.2. The sample 1419.3. Software 1419.4. X-ray study of crinoids 1429.4.1. Presentation and current issue with crinoids 1429.4.2. From radiography to CT scans 1439.4.3. Crinoids and CT scanning at the MNHN: various ongoing projects 1439.5. Conclusion 1509.6. References 150Chapter 10. Conceptual and Methodological Foundations of Integrative Taxonomy 153Aurélien MIRALLES and Nicolas PUILLANDRE10.1. Introduction 15310.2. A multifaceted discipline 15410.2.1. Defining taxonomy 15410.2.2. The two tasks of contemporary α taxonomy 15610.3. A brief history of the taxonomic paradigm, from Linnaeus to the modern world 15810.3.1. Origins 15810.3.2. Evolution(s) 15810.3.3. Renaissance 16010.4. Taxonomy of tomorrow: issues and prospects 16310.5. References 165Chapter 11. Thiomargarita magnifica: A Giant from Marine Mangroves, Pushing the Limits of Bacteriology 171Olivier GROS, Silvina GONZALEZ-RIZZO, Nathalie ELISABETH and Jean-Marie VOLLAND11.1. Introduction 17111.1.1. A diverse bacterial world 17111.1.2. A microbial world is not always microscopic 17211.1.3. Physiological limitations linked to gigantism in bacteria 17211.2. Thiomargarita magnifica 17411.2.1. A giant bacterium 17511.2.2. A bacterium with an exceptional genome 17511.2.3. A bacterium with high cellular complexity 17611.2.4. A giant colonizing the sediments in mangrove swamps in Guadeloupe 17611.3. Conclusion 17911.4. References 180Chapter 12. New Species of Freshwater Fish in France: Reasons and Impacts for Management 183Gaël DENYS, Agnès DETTAÏ, Henri PERSAT, Nicolas POULET and Philippe KEITH12.1. Introduction 18312.2. Reasons for these changes 18712.2.1. Taking account of biogeographical context 18712.2.2. The concept of a species and the approach of integrative taxonomy 19212.3. Impacts on management 19312.4. Conclusion 19512.5. References 196Chapter 13. Effects of Sampling Bias in Estimating Phylodiversity in the Southern Ocean 201Anna KONDRATYEVA13.1. Why study the Southern Ocean and its biodiversity? 20113.2. Knowledge of marine biodiversity in the Southern Ocean 20213.3. Sampling bias in data on Antarctic marine biodiversity 20313.4. Biodiversity measurements for the Southern Ocean 20413.5. Effects of sampling bias on the calculation of phylodiversity indices 20613.5.1. Taxonomic shortfall and phylodiversity 20613.5.2. Evolutionary shortfall and phylodiversity 20713.5.3. Spatial shortfall and phylodiversity 20913.6. Conclusion 21113.7. References 212Chapter 14. Standardization, Accessibility of Research Data and Open Science 217Visotheary UNG14.1. Why talk about standards, open data and open science? 21714.1.1. Issues 21814.1.2. French national context. 21914.1.3. International context 22014.2. How can we ensure FAIR data in practice? 22114.2.1. Draw inspiration from what exists already 22114.2.2. Implementing standards 22214.2.3. Biodiversity Informatics 22314.3. Where can research data be stored? Data warehouses and data papers 22714.4. Conclusion 22914.4.1. From the need to shift the sociocultural paradigm… 22914.4.2. …to more ethical research 23014.5. References 231List of Authors 237Index 243