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Inventory of Biodiversity Today
New Methods and Discoveries
Violaine Nicolas (Edited by), Nicolas (Author)
9781786309587, Wiley
Hardback, published 17 September 2024
272 pages
23.5 x 15.6 x 1.8 cm, 0.491 kg
Our knowledge of living organisms is still very limited, with less than 20% of the world’s species known to date. It is therefore essential to increase our efforts to inventory biodiversity. This is the goal of scientific research, but it is also a vital responsibility in the face of the sixth extinction. With so many species set to disappear before they can be analyzed, the compilation of this inventory now represents a major challenge. Thanks to the collaborative work of numerous researchers from the Institut de systématique, évolution, biodiversité (ISYEB) and other institutions, Inventory of Biodiversity Today presents the latest methods of field data collection and analysis. Strategies have diversified and are providing new and ever-more-precise data on a growing number of specimens. All of these data are integrated to delimit and describe living species, and are accessible to as many people as possible, so we can all take action on a daily basis to better understand and preserve our planet.
Introduction xiii Chapter 1. Scientific Exploration Campaigns to Inventory Existing Biodiversity and Hasten the Discovery of New Species 1 1.1. Introduction 1 1.2. A historical overview of diversity inventory 2 1.3. The advent of molecular taxonomy 3 1.4. Biodiversity: the emergence of a concept in the face of the crisis 4 1.5. An incomplete inventory of diversity 5 1.6. The place of scientific exploration campaigns, run by the French Natural History Museum, in the inventory of biodiversity 6 1.7. Innovations to speed up the description of species 7 1.8. Challenges and issues surrounding scientific exploration campaigns 8 1.9. Conclusion 9 1.10. References 9 Chapter 2. Half a Century of Naturalist Exploration of Upper Bathyal Benthic Environments: Ruptures and Continuities 11 2.1. The deep ocean: we have barely begun to plumb the depths 11 2.2. The Tropical Deep-Sea Benthos program 12 2.2.1. From MUSORSTOM to Tropical Deep-Sea Benthos 12 2.2.2. TDSB campaigns across time and space 13 2.2.3. Program metrics 19 2.3. Continuity and ruptures in the TDSB program 19 2.3.1. The place of "living fossils" in discourse on the deep oceans 19 2.3.2. A program evolving with societal issues 21 2.4. Campaigns at sea with taxonomic results: a network dynamic around naturalist collections 22 2.5. References 23 Chapter 3. CEAMARC: An Integrated Campaign to Evaluate Biodiversity at All Scales in Adélie Land 27 3.1. Introduction 27 3.2. The CEAMARC expedition (Collaborative East-Antarctic Marine Census) 29 3.2.1. An "integrated" campaign 29 3.2.2. Sampling methods 31 3.3. Some results 34 3.4. Conclusion 36 3.5. References 37 Chapter 4. Objectif Plancton: A Citizen Science Program to Study Plankton Diversity 41 4.1. A citizen science project 41 4.2. Scientific objectives 43 4.3. Materials and methodology 45 4.4. Avenues of research 49 4.4.1. Ichthyoplankton 49 4.4.2. Phytoplankton 51 4.4.3. Human and social sciences 53 4.5. Conclusion 55 4.6. References 56 Chapter 5. Environmental DNA for Observing Marine Mammals in the Marine Protected Areas of Iroise and the Antilles 59 5.1. Introduction 59 5.2. Studying cetaceans in order to know them better: from visual observation to DNA analysis 61 5.3. Progress in approaches using environmental DNA (eDNA) and metabarcoding 62 5.4. Detection of marine mammals by eDNA analysis 63 5.5. First campaign in the Iroise Sea, 2019-2020 64 5.6. The An Bad’lo campaign in Martinique 66 5.7. Detection of marine mammals and other mobile marine fauna through the study of eDNA: from naturalist inventories to the support of public policies 68 5.8. References 69 Chapter 6. DNA Barcoding for Identifying Species and Monitoring French Biodiversity 73 6.1. Introduction 73 6.2. DNA barcoding for species identification 75 6.2.1. A simple and standardized tool for molecular identification 75 6.2.2. From the specimen to the community: identification by DNA barcoding and metabarcoding 76 6.2.3. DNA barcodes of the living world: a collective and international effort 79 6.3. DNA barcode libraries for biodiversity in Metropolitan France and overseas territories 81 6.4. Main challenges for the molecular identification of species in France 84 6.4.1. Development of exhaustive and accessible reference libraries 84 6.4.2. Molecular identification of species: an asset for monitoring French terrestrial biodiversity 86 6.5. Conclusion and perspectives 88 6.6. References 88 Chapter 7. Exploring the Molecular Biodiversity of Specimens in Collections: The Case of Coccinellidae 95 7.1. Introduction 95 7.2. DNA sequencing of collection specimens 96 7.3. Methodology for DNA sequencing of collection specimens 97 7.3.1. Extraction of DNA from collection specimens 97 7.3.2. Difficulties in the molecular use of collection specimens 97 7.3.3. Next-Generation Sequencing (NGS) technologies used in museomics 98 7.4. Recent results from museomic studies on insects 99 7.5. Context of the study on biodiversity and systematics of Coccinellidae 106 7.5.1. Applications of museomics for exploring the biodiversity of Coccinellidae 107 7.5.2. Barriers to the exploration of Coccinellidae biodiversity 109 7.6. Conclusion 112 7.7. References 112 Chapter 8. New Tools and New Discoveries in Paleo-entomology: Looking to Future Challenges 123 8.1. Insects as essential players in past and present ecosystems 123 8.2. Discovering the past to understand the present (and perhaps predict the future) 125 8.2.1. A science which, until recently, had been largely overlooked 126 8.2.2. Spectacular recent progress in data analysis 127 8.3. Modern information-capture tools 128 8.3.1. Bibliography: "I had a dream" 128 8.3.2. The field 129 8.3.3. Fossil preparation 129 8.3.4. Information capture from fossils 130 8.4. More "exotic" approaches 131 8.4.1. Fossil trophic interactions 131 8.4.2. DNA and organic chemistry 132 8.5. Conclusion 132 8.6. References 133 Chapter 9. X-ray Tomography of Crinoids: Morphological Diversity and Evolution Seen under a Different Light 139 9.1. X-ray microtomography 139 9.2. The sample 141 9.3. Software 141 9.4. X-ray study of crinoids 142 9.4.1. Presentation and current issue with crinoids 142 9.4.2. From radiography to CT scans 143 9.4.3. Crinoids and CT scanning at the MNHN: various ongoing projects 143 9.5. Conclusion 150 9.6. References 150 Chapter 10. Conceptual and Methodological Foundations of Integrative Taxonomy 153 10.1. Introduction 153 10.2. A multifaceted discipline 154 10.2.1. Defining taxonomy 154 10.2.2. The two tasks of contemporary α taxonomy 156 10.3. A brief history of the taxonomic paradigm, from Linnaeus to the modern world 158 10.3.1. Origins 158 10.3.2. Evolution(s) 158 10.3.3. Renaissance 160 10.4. Taxonomy of tomorrow: issues and prospects 163 10.5. References 165 Chapter 11. Thiomargarita magnifica: A Giant from Marine Mangroves, Pushing the Limits of Bacteriology 171 11.1. Introduction 171 11.1.1. A diverse bacterial world 171 11.1.2. A microbial world is not always microscopic 172 11.1.3. Physiological limitations linked to gigantism in bacteria 172 11.2. Thiomargarita magnifica 174 11.2.1. A giant bacterium 175 11.2.2. A bacterium with an exceptional genome 175 11.2.3. A bacterium with high cellular complexity 176 11.2.4. A giant colonizing the sediments in mangrove swamps in Guadeloupe 176 11.3. Conclusion 179 11.4. References 180 Chapter 12. New Species of Freshwater Fish in France: Reasons and Impacts for Management 183 12.1. Introduction 183 12.2. Reasons for these changes 187 12.2.1. Taking account of biogeographical context 187 12.2.2. The concept of a species and the approach of integrative taxonomy 192 12.3. Impacts on management 193 12.4. Conclusion 195 12.5. References 196 Chapter 13. Effects of Sampling Bias in Estimating Phylodiversity in the Southern Ocean 201 13.1. Why study the Southern Ocean and its biodiversity? 201 13.2. Knowledge of marine biodiversity in the Southern Ocean 202 13.3. Sampling bias in data on Antarctic marine biodiversity 203 13.4. Biodiversity measurements for the Southern Ocean 204 13.5. Effects of sampling bias on the calculation of phylodiversity indices 206 13.5.1. Taxonomic shortfall and phylodiversity 206 13.5.2. Evolutionary shortfall and phylodiversity 207 13.5.3. Spatial shortfall and phylodiversity 209 13.6. Conclusion 211 13.7. References 212 Chapter 14. Standardization, Accessibility of Research Data and Open Science 217 14.1. Why talk about standards, open data and open science? 217 14.1.1. Issues 218 14.1.2. French national context. 219 14.1.3. International context 220 14.2. How can we ensure FAIR data in practice? 221 14.2.1. Draw inspiration from what exists already 221 14.2.2. Implementing standards 222 14.2.3. Biodiversity Informatics 223 14.3. Where can research data be stored? Data warehouses and data papers 227 14.4. Conclusion 229 14.4.1. From the need to shift the sociocultural paradigm… 229 14.4.2. …to more ethical research 230 14.5. References 231 List of Authors 237 Index 243
Violaine NICOLAS
Line LE GALL
Sarah SAMADI and Sophie BARY
Marc ELÉAUME, Nadia AMÉZIANE, Frédéric BUSSON, Romain CAUSSE, Agnès DETTAÏ, Guillaume LECOINTRE and Catherine OZOUF-COSTAZ
Cyril 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. SCHNELL
Jean-Luc JUNG
Rodolphe ROUGERIE, Lucas SIRE and Antoine LÉVÊQUE
Karen SALAZAR, Romain NATTIER and Guillaume ACHAZ
André NEL, Patricia NEL, Jean-Paul KUNDURA, Romain GARROUSTE, Valérie NGÔ-MULLER, Mathieu BODERAU, Thomas SCHUBNEL and Corentin JOUAULT
Pablo MARTINEZ-SOARES, Nadia AMÉZIANE, Marta BELLATO, Julien BIGOT, Margot MATHIEU, Michel ROUX, Patricia WILLS and Marc ELÉAUME
Aurélien MIRALLES and Nicolas PUILLANDRE
Olivier GROS, Silvina GONZALEZ-RIZZO, Nathalie ELISABETH and Jean-Marie VOLLAND
Gaël DENYS, Agnès DETTAÏ, Henri PERSAT, Nicolas POULET and Philippe KEITH
Anna KONDRATYEVA
Visotheary UNG
Subject Areas: Biology, life sciences [PS]
