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1. Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts

Author

Florian Baletaud, Gaël Lecellier, Antoine Gilbert, Laëtitia Mathon, Jean-Marie Côme, Tony Dejean, Mahé Dumas, Sylvie Fiat, and Laurent Vigliola

Subjects
conservation, biomass, biodiversity, hotspot, coral reefs, mesophotic slope, Biology (General), QH301-705.5
Abstract

Seamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages across five environments of different depths: coral reefs (15 m), shallow seamounts (50 m), continental slopes (150 m), intermediate seamounts (250 m), and deep seamounts (500 m). We modeled assemblages using 12 environmental variables and found depth to be the main driver of fish diversity and biomass, although other variables like human accessibility were important. Boosted Regression Trees (BRT) revealed a strong negative effect of depth on species richness, segregating coral reefs from deep-sea environments. Surprisingly, BRT showed a hump-shaped effect of depth on fish biomass, with significantly lower biomass on coral reefs than in shallowest deep-sea environments. Biomass of large predators like sharks was three times higher on shallow seamounts (50 m) than on coral reefs. The five studied environments showed quite distinct assemblages. However, species shared between coral reefs and deeper-sea environments were dominated by highly mobile large predators. Our results suggest that seamounts are no diversity hotspots for fish. However, we show that shallower seamounts form biomass oases and refuges for threatened megafauna, suggesting that priority should be given to their protection.

Published
2023
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2. The aesthetic value of reef fishes is globally mismatched to their conservation priorities.

Author

Juliette Langlois, François Guilhaumon, Florian Baletaud, Nicolas Casajus, Cédric De Almeida Braga, Valentine Fleuré, Michel Kulbicki, Nicolas Loiseau, David Mouillot, Julien P Renoult, Aliénor Stahl, Rick D Stuart Smith, Anne-Sophie Tribot, and Nicolas Mouquet

Subjects
Biology (General), QH301-705.5
Abstract

Reef fishes are closely connected to many human populations, yet their contributions to society are mostly considered through their economic and ecological values. Cultural and intrinsic values of reef fishes to the public can be critical drivers of conservation investment and success, but remain challenging to quantify. Aesthetic value represents one of the most immediate and direct means by which human societies engage with biodiversity, and can be evaluated from species to ecosystems. Here, we provide the aesthetic value of 2,417 ray-finned reef fish species by combining intensive evaluation of photographs of fishes by humans with predicted values from machine learning. We identified important biases in species' aesthetic value relating to evolutionary history, ecological traits, and International Union for Conservation of Nature (IUCN) threat status. The most beautiful fishes are tightly packed into small parts of both the phylogenetic tree and the ecological trait space. In contrast, the less attractive fishes are the most ecologically and evolutionary distinct species and those recognized as threatened. Our study highlights likely important mismatches between potential public support for conservation and the species most in need of this support. It also provides a pathway for scaling-up our understanding of what are both an important nonmaterial facet of biodiversity and a key component of nature's contribution to people, which could help better anticipate consequences of species loss and assist in developing appropriate communication strategies.

Published
2022
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3. The distribution of coastal fish <scp>eDNA</scp> sequences in the Anthropocene

Author

Laetitia Mathon, Virginie Marques, Stéphanie Manel, Camille Albouy, Marco Andrello, Emilie Boulanger, Julie Deter, Régis Hocdé, Fabien Leprieur, Tom B. Letessier, Nicolas Loiseau, Eva Maire, Alice Valentini, Laurent Vigliola, Florian Baletaud, Sandra Bessudo, Tony Dejean, Nadia Faure, Pierre‐Edouard Guerin, Meret Jucker, Jean‐Baptiste Juhel, Kadarusman, Andrea Polanco F., Laurent Pouyaud, Dario Schwörer, Kirsten F. Thompson, Marc Troussellier, Hagi Yulia Sugeha, Laure Velez, Xiaowei Zhang, Wenjun Zhong, Loïc Pellissier, David Mouillot, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Dynamique et durabilité des écosystèmes : de la source à l’océan (DECOD), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institute for the Study of the Anthropic Impacts and the Sustainability in the Marine Environment (IAS), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Andromède Océanologie, Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD [France-Ouest]), Zoological Society of London - ZSL (UNITED KINGDOM), The University of Western Australia (UWA), Lancaster Environment Centre, Lancaster University, SPYGEN [Le Bourget-du-Lac], Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Nouvelle-Calédonie]), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC), Fundación Malpelo y Otros Ecosistemas Marinos, Institute of Terrestrial Ecosystems (ITES), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Politeknik Kelautan dan Perikanan Sorong (POLTEK), Programa de Biodiversidad y Ecosistemas Marino, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), University of Exeter, Greenpeace Research Laboratories, Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Universitas Indonesia (UI ), Centre of Chemical Safety and Risks, School of the Environment, Nanjing University, Nanjing University (NJU), and Swiss Federal Institute for Forest, Snow and Landscape Research WSL

Subjects
α- and β-diversity, Global and Planetary Change, Ecology, coastal fish communities, environmental factors, [SDE.MCG]Environmental Sciences/Global Changes, socio-economic factors, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, environmental DNA, Ecology, Evolution, Behavior and Systematics
Abstract

Aim Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors. Location Tropical, temperate and polar coastal areas. Time period Present day. Major taxa studied Marine fishes. Methods We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity. Results We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.

Published
2023

4. Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Author

Laetitia Mathon, Virginie Marques, David Mouillot, Camille Albouy, Marco Andrello, Florian Baletaud, Giomar H. Borrero-Pérez, Tony Dejean, Graham J. Edgar, Jonathan Grondin, Pierre-Edouard Guerin, Régis Hocdé, Jean-Baptiste Juhel, null Kadarusman, Eva Maire, Gael Mariani, Matthew McLean, Andrea Polanco F., Laurent Pouyaud, Rick D. Stuart-Smith, Hagi Yulia Sugeha, Alice Valentini, Laurent Vigliola, Indra B. Vimono, Loïc Pellissier, and Stéphanie Manel

Subjects
coral reef fish, Ecology, General Immunology and Microbiology, Coral Reefs, Fishes, visual census, Biodiversity, General Medicine, biogeographic patterns, DNA, Environmental, General Biochemistry, Genetics and Molecular Biology, eDNA metabarcoding, Animals, Humans, General Agricultural and Biological Sciences, Ecosystem, General Environmental Science
Abstract

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.

Published
2022

6. The aesthetic value of reef fishes is globally mismatched to their conservation priorities

Author

Juliette Langlois, François Guilhaumon, Florian Baletaud, Nicolas Casajus, Cédric De Almeida Braga, Valentine Fleuré, Michel Kulbicki, Nicolas Loiseau, David Mouillot, Julien P. Renoult, Aliénor Stahl, Rick D. Stuart Smith, Anne-Sophie Tribot, Nicolas Mouquet, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Centre de Synthèse et d’Analyse sur la Biodiversité (CESAB), Fondation pour la recherche sur la Biodiversité (FRB), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Nouvelle-Calédonie]), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC), Toxicologie Intégrative & Métabolisme (ToxAlim-TIM), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Temps, espaces, langages Europe méridionale-Méditerranée (TELEMME), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN)

Subjects
Conservation of Natural Resources, General Immunology and Microbiology, Esthetics, Coral Reefs, General Neuroscience, [SDE.MCG]Environmental Sciences/Global Changes, Fishes, Biodiversity, General Biochemistry, Genetics and Molecular Biology, Animals, Humans, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Ecosystem, Phylogeny
Abstract

International audience; Reef fishes are closely connected to many human populations, yet their contributions to society are mostly considered through their economic and ecological values. Cultural and intrinsic values of reef fishes to the public can be critical drivers of conservation investment and success, but remain challenging to quantify. Aesthetic value represents one of the most immediate and direct means by which human societies engage with biodiversity, and can be evaluated from species to ecosystems. Here, we provide the aesthetic value of 2,417 ray-finned reef fish species by combining intensive evaluation of photographs of fishes by humans with predicted values from machine learning. We identified important biases in species’ aesthetic value relating to evolutionary history, ecological traits, and International Union for Conservation of Nature (IUCN) threat status. The most beautiful fishes are tightly packed into small parts of both the phylogenetic tree and the ecological trait space. In contrast, the less attractive fishes are the most ecologically and evolutionary distinct species and those recognized as threatened. Our study highlights likely important mismatches between potential public support for conservation and the species most in need of this support. It also provides a pathway for scaling-up our understanding of what are both an important nonmaterial facet of biodiversity and a key component of nature’s contribution to people, which could help better anticipate consequences of species loss and assist in developing appropriate communication strategies.

Published
2021

7. Circumglobal distribution of fish environmental DNA in coral reefs

Author

Marco Andrello, Florian Baletaud, Loïc Pellissier, Gael Mariani, Rick D. Stuart-Smith, Laurent Vigliola, Giomar Helena Borrero-Pérez, Régis Hocdé, Jonathan Grondin, Alice Valentini, Indra B. Vimono, Hagi Yulia Sugeha, Graham J. Edgar, Jean-Baptiste Juhel, Andrea Polanco F., Laetitia Mathon, David Mouillot, Tony Dejean, Laurent Pouyaud, Virginie Marques, Eva Maire, Stéphanie Manel, Matthew McLean, Camille Albouy, K Kadarusman, Pierre-Edouard Guerin, Institut de Recherche pour le Développement (IRD), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Nouvelle-Calédonie]), Ifremer - Nouvelle-Calédonie, and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Université de la Nouvelle-Calédonie (UNC)

Subjects
0106 biological sciences, Coral reefs, health care facilities, manpower, and services, education, Distribution (economics), Biology, PACIFIQUE, 010603 evolutionary biology, 01 natural sciences, eDNA biodiversity assessment, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, OCEAN INDIEN, MOTUs, Environmental DNA, 14. Life underwater, health care economics and organizations, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, geography, geography.geographical_feature_category, business.industry, 010604 marine biology & hydrobiology, fungi, General Engineering, Marine fish, Coral reef, 15. Life on land, ATLANTIQUE, Fishery, marine fish, %22">Fish , population characteristics, business, geographic locations
Abstract

Coral reefs host the highest fish diversity on Earth despite covering less than 0.1% of the ocean’s seafloor. At the same time they are also extremely threatened. Data syntheses over decades of surveys estimate the total number of coral reef fishes to vary from 2,400 to 8,000 species distributed among roughly 100 families. But this diversity remains largely unknown. Here, we investigated how environmental DNA (eDNA) could describe the distribution of fish diversity in coral reefs. We generated 504,457,267 raw 12S ribosomal DNA (rDNA) sequence reads from 251 samples (2,693 PCR replicates) collected at 25 sites in 145 stations covering five regions across the Indian, Pacific and Atlantic Oceans. Bioinformatic analysis clustered these sequences into 2,160 molecular operational taxonomic units (MOTUs) corresponding to distinct species (Marques 2020) We compared our results, with visual census surveys from Reef Life Survey, on 2,813 transects in tropical regions. Our outcomes demonstrate the capacity of eDNA metabarcoding from water samples to reconstruct well-known biogeographic patterns of fish diversity on coral reefs, such as species richness gradients towards the coral triangle, and family proportion stability across sites (Bellwood and Hughes 2001). Additionally, eDNA survey data documented a higher fish species (16%) and family (50%) diversity than estimates obtained with underwater visual surveys carried out on 20 times more sites. MOTU richness per family retrieved with eDNA closely matched fish species richness within families recorded in visual census data. However, eDNA revealed higher richness of reef-associated species and species from adjacent habitats, of cryptobenthic or nocturnal species, but also of pelagic and wide-ranging species. eDNA survey data showed that fish diversity is characterized by spatially heterogeneous species assemblages among regions, with more dissimilarity among adjacent coral reefs than detected with visual survey data. Unlike visual surveys, eDNA metabarcoding revealed the same prevalence of rarity as expected under the neutral theory of biodiversity, suggesting the predominance of random processes and ecological equivalence within trophic groups at large scale to explain fish biodiversity patterns on coral reefs. Our study demonstrates how sequencing eDNA from water provides a rapid and effective approach to characterize and assess coral reef diversity across large spatial scales, thereby also uncovering hidden biodiversity patterns.

Published
2021

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