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 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