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.
Table of Contents
Introduction xiii
Violaine NICOLAS
Chapter 1. Scientific Exploration Campaigns to Inventory Existing Biodiversity and Hasten the Discovery of New Species 1
Line LE GALL
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
Sarah SAMADI and Sophie BARY
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
Marc ELÉAUME, Nadia AMÉZIANE, Frédéric BUSSON, Romain CAUSSE, Agnès DETTAÏ, Guillaume LECOINTRE and Catherine OZOUF-COSTAZ
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
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
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
Jean-Luc JUNG
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
Rodolphe ROUGERIE, Lucas SIRE and Antoine LÉVÊQUE
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
Karen SALAZAR, Romain NATTIER and Guillaume ACHAZ
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
André NEL, Patricia NEL, Jean-Paul KUNDURA, Romain GARROUSTE, Valérie NGÔ-MULLER, Mathieu BODERAU, Thomas SCHUBNEL and Corentin JOUAULT
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
Pablo MARTINEZ-SOARES, Nadia AMÉZIANE, Marta BELLATO, Julien BIGOT, Margot MATHIEU, Michel ROUX, Patricia WILLS and Marc ELÉAUME
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
Aurélien MIRALLES and Nicolas PUILLANDRE
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
Olivier GROS, Silvina GONZALEZ-RIZZO, Nathalie ELISABETH and Jean-Marie VOLLAND
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
Gaël DENYS, Agnès DETTAÏ, Henri PERSAT, Nicolas POULET and Philippe KEITH
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
Anna KONDRATYEVA
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
Visotheary UNG
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
