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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
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.
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Veröffentlichungsjahr: 2024
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Table of Contents
Cover
Table of Contents
Title Page
Copyright Page
Introduction Inventory of Biodiversity Today: New Methods and Discoveries
1 Scientific Exploration Campaigns to Inventory Existing Biodiversity and Hasten the Discovery of New Species
1.1. Introduction
1.2. A historical overview of diversity inventory
1.3. The advent of molecular taxonomy
1.4. Biodiversity: the emergence of a concept in the face of the crisis
1.5. An incomplete inventory of diversity
1.6. The place of scientific exploration campaigns, run by the French Natural History Museum, in the inventory of biodiversity
1.7. Innovations to speed up the description of species
1.8. Challenges and issues surrounding scientific exploration campaigns
1.9. Conclusion
1.10. References
2 Half a Century of Naturalist Exploration of Upper Bathyal Benthic Environments: Ruptures and Continuities
2.1. The deep ocean: we have barely begun to plumb the depths
2.2. The Tropical Deep-Sea Benthos program
2.3. Continuity and ruptures in the TDSB program
2.4. Campaigns at sea with taxonomic results: a network dynamic around naturalist collections
2.5. References
3 CEAMARC: An Integrated Campaign to Evaluate Biodiversity at All Scales in Adélie Land
3.1. Introduction
3.2. The CEAMARC expedition (Collaborative East-Antarctic Marine Census)
3.3. Some results
3.4. Conclusion
3.5. References
4 Objectif Plancton: A Citizen Science Program to Study Plankton Diversity
4.1. A citizen science project
4.2. Scientific objectives
4.3. Materials and methodology
4.4. Avenues of research
4.5. Conclusion
4.6. References
5 Environmental DNA for Observing Marine Mammals in the Marine Protected Areas of Iroise and the Antilles
5.1. Introduction
5.2. Studying cetaceans in order to know them better: from visual observation to DNA analysis
5.3. Progress in approaches using environmental DNA (eDNA) and metabarcoding
5.4. Detection of marine mammals by eDNA analysis
5.5. First campaign in the Iroise Sea, 2019–2020
5.6. The An Bad’lo campaign in Martinique
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
5.8. References
6 DNA Barcoding for Identifying Species and Monitoring French Biodiversity
6.1. Introduction
6.2. DNA barcoding for species identification
6.3. DNA barcode libraries for biodiversity in Metropolitan France and overseas territories
6.4. Main challenges for the molecular identification of species in France
6.5. Conclusion and perspectives
6.6. References
7 Exploring the Molecular Biodiversity of Specimens in Collections: The Case of Coccinellidae
7.1. Introduction
7.2. DNA sequencing of collection specimens
7.3. Methodology for DNA sequencing of collection specimens
7.4. Recent results from museomic studies on insects
7.5. Context of the study on biodiversity and systematics of Coccinellidae
7.6. Conclusion
7.7. References
8 New Tools and New Discoveries in Paleo-entomology: Looking to Future Challenges
8.1. Insects as essential players in past and present ecosystems
8.2. Discovering the past to understand the present (and perhaps predict the future)
8.3. Modern information-capture tools
8.4. More “exotic” approaches
8.5. Conclusion
8.6. References
9 X-ray Tomography of Crinoids: Morphological Diversity and Evolution Seen under a Different Light
9.1. X-ray microtomography
9.2. The sample
9.3. Software
9.4. X-ray study of crinoids
9.5. Conclusion
9.6. References
10 Conceptual and Methodological Foundations of Integrative Taxonomy
10.1. Introduction
10.2. A multifaceted discipline
10.3. A brief history of the taxonomic paradigm, from Linnaeus to the modern world
10.4. Taxonomy of tomorrow: issues and prospects
10.5. References
11
Thiomargarita magnifica
: A Giant from Marine Mangroves, Pushing the Limits of Bacteriology
11.1. Introduction
11.2. Thiomargarita magnifica
11.3. Conclusion
11.4. References
12 New Species of Freshwater Fish in France: Reasons and Impacts for Management
12.1. Introduction
12.2. Reasons for these changes
12.3. Impacts on management
12.4. Conclusion
12.5. References
13 Effects of Sampling Bias in Estimating Phylodiversity in the Southern Ocean
13.1. Why study the Southern Ocean and its biodiversity?
13.2. Knowledge of marine biodiversity in the Southern Ocean
13.3. Sampling bias in data on Antarctic marine biodiversity
13.4. Biodiversity measurements for the Southern Ocean
13.5. Effects of sampling bias on the calculation of phylodiversity indices
13.6. Conclusion
13.7. References
14 Standardization, Accessibility of Research Data and Open Science
14.1. Why talk about standards, open data and open science?
14.2. How can we ensure FAIR data in practice?
14.3. Where can research data be stored? Data warehouses and data papers
14.4. Conclusion
14.5. References
List of Authors
Index
Other titles from iSTE in Biology and Biomedical Engineering
End User License Agreement
List of Tables
Chapter 2
Table 2.1. List of TDSB campaigns from 1976 to 2021. The names of the most pro...
Chapter 6
Table 6.1. Overview, for the five main groups of eukaryotes considered, of the...
Chapter 7
Table 7.1. Sequencing of historical DNA from some of the most ancient insect s...
Chapter 12
Table 12.1. List of the systematic differentiations and taxonomic changes in t...
List of Illustrations
Chapter 2
Figure 2.1. Geographic distribution of campaigns run between 1976 and 2021.
Figure 2.2. Cumulative curves showing the number of publications per year for ...
Figure 2.3. Word cloud created from the titles of the 348 articles published a...
Chapter 3
Figure 3.1. Map of the sea around Dumont d’Urville, including the main toponym...
Figure 3.2. Some of the gear deployed during the CEAMARC expedition: a) a beam...
Figure 3.3. Proposed areas for the CCAMLR and marine protected areas in the So...
Chapter 4
Figure 4.1. The Objectif Plancton “ecosystem”.
Figure 4.2. The three sites studied by Objectif Plancton.
Figure 4.3. Sampling points in Brest roadstead (1), Concarneau Bay (2), and Lo...
Figure 4.4. Morphological identification of fish larvae and a few examples of ...
Figure 4.5. Nanophytoplankton: chain of Chaetoceros cf debilis, (10 µm per cel...
Figure 4.6. Microphytoplankton: Striatella unipunctata, (around 100 µm in side...
Chapter 5
Figure 5.1. Distribution of the sampling sites in the Iroise Sea and in Brest ...
Figure 5.2. Location, name, sampling date and depth at the nine sites studied ...
Chapter 6
Figure 6.1. Diagrammatic represention of the process of molecular identificati...
Figure 6.2. Development of BOLD since its creation in 2005: a) evolution of th...
Figure 6.3. Radar charts representing the level of completeness (shaded area, ...
Figure 6.4. Operational test of a device for monitoring insect populations in ...
Chapter 7
Figure 7.1. Number of articles published using historical DNA from insects pre...
Figure 7.2. Map of the mitochondrial genome of a) Coccidophilus cariba and b) ...
Figure 7.3. Venn diagram showing the number of COI gene sequence records and t...
Chapter 8
Figure 8.1. An ant of the genus Fallomyrma sp. (Baltic amber, Priabonian) (col...
Figure 8.2. Phylogenetic hypothesis for Odonatoptera (superorder containing mo...
Figure 8.3. Number of publications in taxonomy of insects and the proportion i...
Figure 8.4. Number of publications on fossilized insects per year (analysis by...
Figure 8.5. Close-up view of the antenna of Thysanoptera Uzelothrips eocenicus...
Figure 8.6. Photograph and 3D reconstruction from microtomography of a Blattod...
Chapter 9
Figure 9.1. Diagrammatic representation of the process of computed tomography,...
Figure 9.2. Reconstructions of fossils found in marl in Possagno (Italy): a) C...
Figure 9.3. Comparison of a juvenile and an adult specimen of Holopus alidis. ...
Figure 9.4. Observations in an adult H. Alidis exploiting different capabiliti...
Figure 9.5. Scans of different lineages of Notocrinus assessed with molecular ...
Chapter 10
Figure 10.1. The main task of alpha taxonomy is species delimitation. Increasi...
Figure 10.2. Reconciling the discontinuity present in the living world with it...
Chapter 11
Figure 11.1. The giant bacterium Thiomargarita magnifica in its coastal marine...
Figure 11.2. Overview of the sulfur cycle in mangrove sediments.
Chapter 12
Figure 12.1. Evolution of the number of freshwater fish species recorded in Fr...
Figure 12.2. France in the Miocene (a) and in the Pliocene (b); source: Persat...
Figure 12.3. France during the last glacial maximum of the Pleistocene. Adapte...
Figure 12.4. Histogram representing the number of freshwater fish species that...
Chapter 14
Figure 14.1. Illustration of the Turing Way project by Scriberia (this illustr...
Figure 14.2. Interest groups and working groups of Biodiversity Information St...
Figure 14.3. Steps in the creation of a standard.
Figure 14.4. Be FAIR and CARE (Caroll et al. 2020, 2022a, 2022b).
Guide
Cover Page
Table of Contents
Title Page
Copyright Page
Introduction
Begin Reading
List of Authors
Index
Other titles from iSTE in Biology and Biomedical Engineering
WILEY END USER LICENSE AGREEMENT
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Series EditorMarie-Christine Maurel
Inventory of Biodiversity Today
New Methods and Discoveries
Edited by
Violaine Nicolas
First published 2024 in Great Britain and the United States by ISTE Ltd and John Wiley & Sons, Inc.
Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the Copyright, Designs and Patents Act 1988, this publication may only be reproduced, stored or transmitted, in any form or by any means, with the prior permission in writing of the publishers, or in the case of reprographic reproduction in accordance with the terms and licenses issued by the CLA. Enquiries concerning reproduction outside these terms should be sent to the publishers at the undermentioned address:
ISTE Ltd27-37 St George’s RoadLondon SW19 4EUUK
www.iste.co.uk
John Wiley & Sons, Inc.111 River StreetHoboken, NJ 07030USA
www.wiley.com
© ISTE Ltd 2024The rights of Violaine Nicolas to be identified as the author of this work have been asserted by her in accordance with the Copyright, Designs and Patents Act 1988.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s), contributor(s) or editor(s) and do not necessarily reflect the views of ISTE Group.
Library of Congress Control Number: 2024938962
British Library Cataloguing-in-Publication DataA CIP record for this book is available from the British LibraryISBN 978-1-78630-958-7
IntroductionInventory of Biodiversity Today: New Methods and Discoveries
Today, as we face the prospect of the sixth mass extinction, the term “biodiversity” has gained popularity, and is widely used. Coined in the 1980s (Wilson 1988), the word is a contraction of the phrase “biological diversity”. At the Earth Summit in Rio de Janeiro in 1992, its definition was set in stone:
‘Biological diversity’ means the variability among living organisms from all sources including, inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems.
Today, we know of only 2.2 million species (Roskov et al. 2014), which is around 20% of the 11 million species estimated to exist. Certain studies – notably those which take account of microbial diversity – place the number far higher, proposing that there are somewhere between one and six billion species (Larsen et al. 2017). In addition, often, we have very limited knowledge of these species. With respect to over half the known macro-organisms, we have only brief descriptions found in dated publications; with respect to unculturable microbes, we are only aware of a few molecules (Troudet et al. 2017).
At the present juncture, it is absolutely crucial that we step up the work of inventorying our world’s biodiversity, with a view to describing the remaining 80% +/–, not only to assuage our own thirst for knowledge and understanding of the world around us and how it evolves, but also because such knowledge could have very concrete implications in our day-to-day lives. For example, recent work has shown that previously unknown, or poorly known, organisms may have critical importance for our societies. The recent Covid-19 pandemic, which brought the world to a standstill for months on end, is an unfortunate example. It shed light on how little we understand the wide variety of coronaviruses and their hosts (Hassanin et al. 2020). Issues such as this may affect not only human health, but also the health of the plants we eat. Think for example, of the plant viruses and viroids about which little is known, but which have been seen to devastate certain crops (Maurel 2018). In addition, it has recently been shown that certain poorly understood micro-organisms have a major role to play in the biogeochemical cycles which govern our world, such as the carbon cycle, the methane cycle, the nitrogen cycle or the sulfur cycle (Lannes et al. 2021). Biodiversity is crucial for us in our daily lives: the oxygen we breathe; the food and water we consume; the drugs which treat our ills; the raw materials we use to clothe ourselves (cotton, hemp, wool, etc.) or build shelters (wood); crop pollination; soil fertilization; climate regulation; soil formation and prevention of soil erosion; the natural purification of water by plants in humid environments; the prevention of water rises and floods by wetlands. All of this is gifted by nature (Grandcolas and Marc 2023). Plainly then, describing and understanding this biodiversity is crucial for our very survival.
How, though, are we to approach this gargantuan task of describing the myriad species, while the number of taxonomists – scientists specializing in this domain – is constantly decreasing? Each year, between 15,000 and 20,000 new species are described by between 30,000 and 40,000 taxonomists, both professional and amateurs; this equates to around one new species every 30 minutes (Miralles et al. 2020). Thus, at the current rate, it would take at least several centuries to fully accomplish the task of completing all taxonomic descriptions (Costello et al. 2013). However, looking down the barrel of the sixth mass extinction event, we realize that time is a luxury we do not have. Numerous species – the majority of species, even – are likely to die out before they can be described, similarly to what are known as the “dark extinctions” of the pre-taxonomic period, before the 1800s (Boehm and Cronk 2021).
The aim of this book is to demonstrate how today’s scientists go about dealing with this immense task. In particular, the approach involves organizing large-scale exploration and inventorying campaigns, which may take place in locations and environments that are nearby and easily accessible, or that are distant or difficult to access such as the ocean depths or the poles. Another strategy is to set up participative science projects, in which ordinary citizens are invited to contribute to the data collection. There are a wide variety of methods used to collect and analyze samples, and numerous forms of data associated with specimens are now systematically recorded (e.g. temperature, pH, conductivity, salinity and turbidity of the water, current direction and velocity, partial pressure of dissolved gases), so as to better understand the interactions between the organisms and their environment. In addition, new methods of data acquisition and processing have been developed, enabling scientists to acquire increasingly precise and unprecedented morphological or genetic data, on an ever-growing number of specimens. For instance, computed microtomography, using X-rays, allows us to view the internal microstructures and create 3D models of these anatomic structures, on both current and fossilized specimens, without causing physical damage to the specimens. Observation with ultraviolet light and environmental scanning electron microscopy (ESEM) also give us access to morphological details without harming the specimens. Approaches based on genetic data have also flourished, and today, they can be used to acquire essential biodiversity data not just from specimens preserved, for varying periods of time, in the collections of natural history museums (barcoding, museum genomics), but also directly from environmental samples such as water or soil samples (metabarcoding).
The development of all of these techniques means that, today, it is possible to generate a vast quantity of data on specimens, which must then be interwoven to define and describe the various species, by means of integrative taxonomy.
Thanks to scientists’ activity and recent technical advances, today we are producing unprecedented quantities of data, which need to be better handled and exploited, taking account of potential sources of skew. In order to better exploit these data sources, it is essential to continue to develop open science, which is a means of conducting research combining production and widespread dissemination, with the goal being to enable as many people as possible to freely access, reuse, build and distribute these resources, unencumbered. Not only does such an approach allow scientists in varying disciplines to pool their knowledge in order to answer complex questions, it also popularizes the research results, so that all of society can have access to them, make use of them, and contribute to the process, be it during the acquisition or data analysis phase.
References
Boehm, M.M.A. and Cronk, Q.C.B. (2021). Dark extinction: The problem of unknown historical extinctions.
Biol. Lett.
, 17(3), 20210007.
Costello, M.J., May, R.M., Stork, N.E. (2013). Can we name Earth’s species before they go extinct?
Science
, 339(6118), 413–416.
Grandcolas, P. and Marc, C. (2023).
Tout comprendre (ou presque) sur la biodiversité
. CNRS Éditions, Paris.
Hassanin, A., Grandcolas, P., Veron, G. (2020). Covid-19: Natural or anthropic origin?
Mammalia
, 85(1), 1–7.
Lannes, R., Cavaud, L., Lopez, P., Bapteste, E. (2021). Marine ultrasmall prokaryotes likely affect the cycling of carbon, methane, nitrogen, and sulfur.
Genome Biol. Evol.
, 13(1), evaa261.
Larsen, B.B., Miller, E., Rhodes, M.K., Wiens, J.J. (2017). Inordinate fondness multiplied and redistributed: The number of species on earth and the new pie of life
. Q. Rev. Biol.
, 92(3), 229–265.
Maurel, M.-C. (2018). À la frontière du vivant : les viroïdes.
The Conversation
[Online]. Available at:
https://theconversation.com/a-la-frontiere-du-vivantles-viro-des-90500
.
Miralles, A., Bruy, T., Wolcott, K., Scherz, M.D., Begerow, D., Beszteri, B., Bonkowski, M., Felden, J., Gemeinholzer, B., Glaw, F. et al. (2020). Repositories for taxonomic data: Where we are and what is missing?
Syst. Biol.
, 69(6), 1231–1253.
Roskov, Y., Kunze, T., Orrell, T., Abucay, L., Paglinawan, L., Culham, A., Bailly, N., Kirk, P.M., Bourgoin, T., Baillargeon, G. et al. (2014).
Species 2000 & ITIS Catalogue of Life, 2014 Annual Checklist
. Naturalis, Leiden.
Troudet, J., Grandcolas, P., Blin, A., Vignes-Lebbe, R., Legendre, F. (2017). Taxonomic bias in biodiversity data and societal preferences.
Sci. Rep.
, 7(1), 9132.
Wilson, E.O. (1988)
. Biodiversity
. National Academy Press, Washington.
Note
Introduction by Violaine NICOLAS.
1Scientific Exploration Campaigns to Inventory Existing Biodiversity and Hasten the Discovery of New Species
1.1. Introduction
Life on Earth first emerged at least 3.5 billion years ago. Since then, it has been constantly evolving, which has led to the phenomena of both diversification and extinction. The fossil records of marine and terrestrial organisms show that the diversity of life, both in the seas and on land, increased exponentially after the end of the Precambrian (Benton 1995), 540 million years ago. Such diversification, though, was punctuated by mass extinctions; the term “biotic crisis” is also employed. Most such extinction events struck marine and terrestrial organisms simultaneously. Within the geological time scale (Bergström et al. 2009), we see no fewer than five major crises, occurring during the Ordovician, the Devonian, the Permian, the Triassic–Jurassic transition and the Cretaceous–Tertiary transition. For example, the Permian–Triassic extinction, which took place some 252 million years ago, saw 95% of marine species and 70% of terrestrial species die out. During the Cretaceous–Tertiary extinction 66 million years ago, during which the dinosaurs rapidly perished, the mammals – who, up until that point, had coexisted with the dinosaurs – suddenly had the place to themselves (so to speak), and we see the group massively diversify. It is plain that the variety of living organisms on planet Earth has resulted from a lengthy and gradual, dynamic process, punctuated by crises. For over a quarter of a century, researchers have been asking whether the particularly proliferous demographic expansion of humans during the Holocene has profoundly altered Earth itself (Myers 1990), leading to a sixth mass extinction event. The extinction rates calculated by biologists tend to demonstrate that this crisis will occur at an even faster rate than the previous five biotic crises (Barnosky et al. 2011), erasing the planet’s biological heritage even before it has been fully described.
1.2. A historical overview of diversity inventory
Reindeer, aurochs, mammoths, horses, bison… as early as 18,000 years ago, our prehistoric ancestors made paintings of animals. Whilst we do not yet know, in detail, what these paintings signified, it is undeniable that they constitute the earliest form of inventory of the surrounding biological diversity. Even in the earliest known literary work, the Epic of Gilgamesh (18th century BCE), the landscape in which the action takes place is described using imagery of fauna (for example, the buffalo) and flora (for example, the cedar). In Ancient times, Aristotle (384–322 BCE), in the Organon, devotes a great deal of time to the observation of animated beings (animals), drawing a contrast with inanimate beings (plants). Aristotle’s pupil, Theophrastus (372–288 BCE), followed in Aristotle’s footsteps, and in particular, developed the discipline of botany, producing a reasoned inventory of the plant life found in the Mediterranean Basin. These two authors offer us detailed observations and descriptions of various animal and plant species; they began to document and classify plants and animals. From the 16th century onward, major explorations by sea led to the discovery of new lands and previously unknown species. By way of example, Captain James Cook’s voyages in the 18th century greatly enriched our knowledge of biodiversity; Cook brought back numerous specimens, which needed to be named. Around the same time, a method emerged for scientific description of the living world, gradually coalescing into classification and nomenclature systems with which to organize known species. The seminal work of Carl Linnaeus (also known as Carl von Linné), Systema Naturae, published in 1735, laid the foundations for modern taxonomy and greatly simplified the way in which species were named, proposing the binomial system and comprising a genus name, followed by a species label. This did away with the lengthy descriptive names in use until that point. The most active period for species description was the 19th century; the natural history collections of the major museums are extremely rich in specimens from that period, which was marked by large-scale scientific expeditions. Charles Darwin’s observations during his voyage aboard the HMS Beagle are famed, in view of the major advances they brought about in the understanding of the evolution and diversity of species. This work led to the publication of Darwin’s On the Origin of Species in 1859, advancing a convincing scientific theory on the origin of the diversity of the living world. France also played an important part: numerous explorations greatly enriched the collections of the National Museum of Natural History. These included Napoleon Bonapart’s Egyptian Campaign (1798–1801), which included academics and artists who were charged with studying and documenting the history, architecture, fauna, flora and culture of Ancient Egypt. The expedition of La Coquille (1822–1825) is another example. Under the command of Louis-Isidore Duperrey, La Coquille sailed the seas of the world, notably focusing on the Pacific Ocean and the islands of the South Pacific. Naturalist research was carried out jointly by Jules Dumont d’Urville, who was in charge of botany and entomology, and René Primevère Lesson, who was in charge of zoology. These studies led to the discovery of numerous new species. After the tropics, its was the poles which captured explorers’ attention, around 1900. In France, Commander Jean-Baptiste Charcot set out to explore both the South and the North Pole. The two World Wars hindered scientific exploration, but also led to major technological breakthroughs, such as the development of electron microscopy. Thereafter, biologists have largely turned their attention to the study of biochemistry and cell biology, to the detriment of species inventory.
1.3. The advent of molecular taxonomy
The discovery of DNA as the carrier of genetic information, and then the discovery of its structure, but above all, the invention of DNA sequencing techniques in the 1970s (Sanger et al. 1977), were giant leaps forward in molecular biology and genomics. DNA sequencing greatly changed the way in which we understood biodiversity, revealing entire sectors of the living world, thanks to phylogenetic methods, which can compare similar DNA sequences with a view to inferring the evolutionary links between specimens. These methods soon led to the discovery of a third domain of the living world: Archaea (Woese and Fox 1977), which, alongside true bacteria, make up the group of procaryotes (i.e. cells without a nucleus), in contrast to eucaryotes (cells which do have a nucleus). Aside from the discovery of this new sector of the living world, the use of DNA sequences as markers to differentiate species considerably sped up the scientific inventory of biodiversity, notably revealing a number of new cryptic species (Blaxter 2004). Paul Hebert (Hebert et al. 2003) proposed using DNA sequences in the same way as a barcode is used in the commercial world, to identify organisms, and thus create a library of the living (Le Gall et al. 2017). Utilizing technological advances, which allow for the handling of massive databases of sequences, the “Earth BioGenome” project (Lewin et al. 2022) aims to create a library, not for short genetic sequences, but for complete reference genomes (Earth BioGenome Project n.d.). In France, the ATLASea project will contribute to the broader international project, by sequencing the reference genome for 4,500 marine organisms.
1.4. Biodiversity: the emergence of a concept in the face of the crisis
The term “biodiversity”, which is now widely used, is a very recent concept, which emerged some thirty years ago, when we became aware of the looming threat of an ecological crisis, caused by human activities. Raymond F. Dasmann is credited with coining the term “biological diversity” (Dasmann 1970), which was then taken up by Thomas Lovejoy, the then-Director of the World Wildlife Fund-US conservation program, who used the term in two 1980 publications. However, it was the Convention on Biological Diversity, ratified at the Earth Summit in Rio de Janeiro in 1992, that popularized the term “biological diversity”, defining it as follows:
‘Biological diversity’ means the variability among living organisms from all sources including, inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems.
The contracted form of “biological diversity” as “biodiversity” then gained widespread use. It is also a concept which has been enriched over time and now, beyond referring to the diversity of the living world, it also includes the way in which we perceive that biodiversity, and in particular, the functions and uses we make of it, not forgetting the symbolic aspects attaching to it.
The Convention on Biological Diversity also established a framework for research and training (article 12), which stipulates that each signatory country shall: “Establish and maintain programmes [sic] for scientific and technical education and training in measures for the identification, conservation and sustainable use of biological diversity”. Though numerous programs and initiatives the world over are devoted to the task, the inventory of biodiversity is far from complete.
1.5. An incomplete inventory of diversity
Inventorying biodiversity consists of identifying and cataloging the species present in a given ecosystem. From the highest peaks on the planet to the deepest trenches of the oceans, to-date, scientists have recorded some two million species (ITIS SPECIES 2000, 2019; Annual Checklist: https://www.catalogueoflife.org/) inhabiting Earth. Of these, 1.3 million are animals, 375,000 are plants (Christenhusz and Byng 2016), 135,000 are fungi, 10,000 are bacteria, 3,000 are viruses, and the remaining 27,000 are chiefly single-celled organisms, often grouped together under the umbrella term Protist, which inadequately reflects their broad divergence, as they account for some ten evolutionary lineages (Adl et al. 2019); they are often as different from one another as plants are from animals.
On average, 18,000 new species are described each year (around 2,300 of these being marine species (Bouchet et al. 2023)), so plainly, the inventory of existing biodiversity is nowhere near complete. Whilst it is a time-consuming task to catalog the species which have been formally described to-date, estimating the number of species yet to be described is a risky business. In the 1980s, Terry Erwin (1982) designed an experiment to estimate the diversity of insects. Fumigating the tree canopy in a forest in Panama, he counted the number of insects per species of tree. Then, using the data on the specificity of insects with respect to the trees that they inhabit, he calculated that this group could include up to 30 million species, as opposed to 1.5 million – the generally accepted figure at the time. Since that evaluation, numerous estimations of biodiversity have been carried out, leading to figures which vary by more than an entire order of magnitude. Mora et al. estimate biodiversity at 8.7 ± 1.2 million species, while Larsen et al. estimate the number as being several billion species, the vast majority (70 to 90%) being bacteria.
In parallel to estimations of the number of species present on Earth, there is also the matter of estimating the number of species under threat. The IPBES Report published in 2019 puts forward the worrying figure of one million species under threat of extinction (Tollefson 2019). A recent study seems to suggest that species which have not yet been officially described are even more threatened than those which have (Liu et al. 2022).
In this context, we can clearly understand the urgent need to continue investigating biodiversity, with a view to stepping up the description of new species and swiftly establishing conservation measures to protect that diversity.
1.6. The place of scientific exploration campaigns, run by the French Natural History Museum, in the inventory of biodiversity
Following in a long tradition of naturalist expeditions, the French Natural History Museum runs numerous ambitious scientific exploration programs, all over the world. There is a particular focus on so-called biodiversity hotspots, which are located mainly in the tropical regions (Tittensor et al. 2010). For example, we could point to the Tropical Deep-Sea Benthos program, launched in 1976 with the IRD (Institute for Research and Development), which explores and analyses biodiversity in the deep waters of the intertropical zone. For over 45 years, thousands of operations have been carried out as part of this program, in the Pacific and the Caribbean. The program “La Planète revisitée” (The Planet Revisited), launched by the expedition to Espiritu Santo in 2006, aims to inventory the natural heritage in regions where it is astonishingly rich, exploring both terrestrial and marine biodiversity. Thus, taxonomists have studied forests and coasts from New Caledonia to Guyana, Corsica, Papua New Guinea and Madagascar, with a fine-toothed comb. These programs enrich the collections and focus primarily on taxa which have received little attention because they are often not highly striking; these are known as neglected taxa. Among the numerous targets are lichens, algae, fungi, insects, mollusks, crustaceans, annelids, and many other groups which are even less well known. The specimens harvested continue to enrich collections and scientific research the world over. Since 2010, over 20% of new marine species described in the world have been discovered through the Museum’s campaigns.
1.7. Innovations to speed up the description of species
Exploration of biodiversity is an activity carried out using a methodology and an approach which, all told, have changed little in over two centuries. Even today, it is the variety of techniques for trapping and collecting samples which ensures the success of a campaign! However, numerous recent innovations have helped improve our ability to deploy sampling methods over an extended period of time and an extended space. The sites to be explored are chosen on the basis of increasingly accurate maps, thanks to satellite teledetection techniques, which are capable of acquiring data on a massive scale and in environments which are difficult to access. However, whilst these methods are particularly effective for submerged lands, they are far less effective for oceanic environments, in which bathymetric data are mainly acquired by the use of multibeam sonar, requiring oceanographic vessels to be deployed to acquire the data. In addition, the use of online databases and data-sharing platforms facilitates collaboration among scientists all around the world. This can help to identify the most relevant areas to explore, either because they have had few or no investigations carried out thus far, or else because they have been found to host extraordinary biodiversity.
Once the samples have been collected, taxonomists identify them by studying a range of characteristics. The data collected, including information on habitat, geographic distribution and ecological interactions, are recorded in databases which should, ideally, conform to the FAIR principle (which refers to data that are Findable, Accessible, Interoperable and Reusable). Artificial intelligence (AI) is also being increasingly used to analyze vast quantities of data (the term “big data” is used, as is “high-throughput data”). For example, machine-learning algorithms can be used to rapidly classify images of species, which speeds up the process of identifying organisms in field studies.
Lay citizens can also contribute to the collection of data on biodiversity, which are often beyond the reach of researchers alone. These participatory science projects set up new means of circulation of knowledge between scientists and society at large. They often involve the use of mobile apps to report observations of species, meaning data can be acquired on a large scale as to the distribution of species, and changes over time can be monitored. However, in order to bring about a significant advance in the description of biodiversity, they must, beyond simple observation, allow for sampling of material which can serve as the basis for the descriptions imposed by the nomenclature codes governing the description of new species. For instance, to supplement operations as part of the “La Planète revisitée” project in New Caledonia, a participatory project known as the “quinzaine des nudibranches” was organized to draw up an inventory of sea slugs. Divers are fascinated by these organisms because of their beauty, original shapes and vibrant colors. In total, 28 local naturalists actively participated in this quest, requiring good training to locate the individuals, as the animals are timid by nature. The involvement of these aware volunteers represented the equivalent of 263 people per day across 50 sites on the Nouméa Peninsula, the lagoon and the reef barrier. With the support of seven researchers, one of whom is a renowned specialist on sea slugs, their work helped to document 352 species, around 80 of which were new, a priori. This experiment in participatory inventory proved to be highly fruitful, and it would be worth repeating in other territories or other seasons.
1.8. Challenges and issues surrounding scientific exploration campaigns
The organizing of scientific explorations involves overcoming still more challenges. Besides the financial costs and logistical requirements which have always been in place, it is now also crucial to take account of the ethical dimension – notably in relation to the protocols for collection, the use of animals for research purposes, and the rights of local communities. The Nagoya protocol, adopted in 2010, and implemented in 2014, regulates access and benefit-sharing (ABS) stemming from the use of genetic resources and associated traditional knowledge. It structures the relations between suppliers and users of genetic resources and the associated traditional knowledge. In practice, each mission is prepared in consultation with the local actors to construct a shared project in which all parties agree on the objectives, means of action and the way in which the elements collected are to be distributed. The collections and knowledge gleaned from expeditions are made public and accessible to all, in accordance with the open-science approach. Thus, it is crucial to ensure conformity with the regulations at every step of the project – in particular, during collection. Such collection must be respectful of the environment, limiting its environmental impact to the fullest extent possible.
1.9. Conclusion
Scientific exploration campaigns are essential to the work of inventorying the planet’s biodiversity, and encouraging the discovery of new species. However, there is still a long way to go before that inventory will be sufficiently complete to be robust. This lack of completeness is a hindrance to scientists, who may not have a realistic view of the web of interactions amongst species, as they can only look at 10% of those species; it also represents a stumbling block for biologists working in conservation. The IUCN, an international organization which sets a conservation status for threatened or endangered species, only does so for species which have been formally described. Thus, species which have not been described are precluded from conservation measures. It is only by continuing our efforts and continuing to organize scientific exploration campaigns that we can continue to acquire valuable knowledge about our biodiversity, with a view to preserving it, and so, protecting our natural heritage for future generations.
1.10. References
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Note
Chapter written by Line LE GALL.
2Half a Century of Naturalist Exploration of Upper Bathyal Benthic Environments: Ruptures and Continuities
2.1. The deep ocean: we have barely begun to plumb the depths
As can be seen from the current state of political affairs (French Government press releases dated 8 June 2023, and the Secretariat General for the Ocean, dated 21 January 2023), our knowledge of the deep ocean beds, defined as those zones of the ocean where light no longer penetrates to allow photosynthesis, is still highly fragmentary. The question of ocean cartography illustrates this lack of knowledge. The ocean, which covers over 70% of the planet’s surface, has a highly irregular bed. The average depth is around 3,800 meters (as compared to an average altitude of only 850 meters in the case of lands above sea level). However, the estimation of depth of less than 18% of ocean beds has been obtained with a resolution of approximately a kilometer, using an echosounder (Mayer et al. 2018). A fortiori, a very small fraction has been inventoried, with a view to documenting the geological and biological diversity.
Scientific exploration of the fauna inhabiting the ocean bed began with some fortuitous discoveries. For example, we can cite the azoic hypothesis, proposed by Edward Forbes in the 19th century (Anderson and Rice 2006). He observed that the abundance of organisms, collected by fishing equipment up to a depth of around 500 meters, decreased with increasing depth. By statistical extrapolation, he hypothesized that there should be no organisms present beyond a depth of around 600 meters. The formulation of this hypothesis led to the collection of other data: contingently, such as the work of Milne-Edwards, who studied the animals collected along the transoceanic cables, which lived at depths of over 1,000 meters; or in an organized fashion, such as the scientific exploration of the world’s oceans, notably with the iconic Challenger expedition, between 1872 and 1876. During this expedition, the onboard scientists took physical measurements (for example, depths and temperatures) and collected numerous geological and biological samples. These data showed that there are mountains and valleys on the ocean floor, and that whatever the depth, it is populated by a diverse range of organisms, though usually not present in large numbers. During the 20th century, the rollout of new techniques such as echo sounding allowed for more detailed mapping of undersea landscapes. The development of submersible machines enabled images of these landscapes to be captured. The exploration of the large abyssal plains confirmed that there, life is fairly sparse, but that there are “oases” of greater diversity within these deserts. The most striking discovery of such oases, to-date, has been the discovery of hydrothermal vents in the late 1970s: the hydrothermal vents, which lie along the oceanic ridges, release geothermally heated fluids, rich in chemical elements, which tend to be toxic to organisms; nevertheless, these areas are populated by dense fauna, with organisms which, at first glance, are very different to those encountered in other deep-ocean habitats.
Notes
Chapter written by Sarah SAMADI and Sophie BARY.
1
For further details, see the dedicated pages for each campaign, which can be found on:
www.expeditions.mnhn.fr
.
2
See:
www.campagnes.flotteoceanographique.fr
.
3
See:
www.expeditions.mnhn.fr
.
