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8. Mapping marine ecosystem services in a multifunctional seascape: the case of Grande Vasière (Bay of Biscay)

Author

Lavialle, Gaël, Boussarie, Germain, Kopp, Dorothee, Morfin, Marie, Mouchet, Maud A., Lavialle, Gaël, Boussarie, Germain, Kopp, Dorothee, Morfin, Marie, and Mouchet, Maud A.

Abstract

IntroductionCoastal and continental shelf ecosystems are among the most productive, yet exploited, ecosystems. The Grande Vasière (GV) covers most part of the French Northern part of the Bay of Biscay, a crucial fishing ground for metropolitan France. It is the place of numerous uses, especially fishing, and will soon shelter sand extraction activities and offshore windfarms. All these activities may compete for space and resources and put pressure on habitats, biodiversity and subsequent ecosystem services (ES). Current management strategies integrate these activities and biodiversity conservation schemes but no ES. MethodsTo fill that gap, we quantified and mapped nine indicators of ecosystem processes (EP), used as proxies of four ES (i.e. sea food provisioning, biological control, regulation of environmental conditions and life cycle maintenance). Due to the complexity of ES, we investigated several EP by ES. Then we identified hotspots and coldspots of supply and spatial overlap among EP and other uses (conservation, fishing, offshore windfarms and sand extraction). ResultsEP mapping suggests a higher capacity of supply of the chosen ES in the Northern part of the GV. We found a strong spatial heterogeneity among the EP related to the same ES, underlining a point of vigilance when designing management measures to sustain ES supply. Northern EP hotspots overlap with high amounts of bottom trawl fishing effort. Higher levels of commercial species diversity and sole spawning grounds in the South overlap with higher amounts of gillnet fishing effort. Areas of sand extraction prospection and offshore windfarms under construction should not overlap with hotspots of EP, at the exception of the sole spawning ground and the commercial species diversity hotspots. Finally, we highlight an overlap of more than 20% of four EP hotspots with Natura 2000 areas, while the Marine Natural Park in the South covers more EP coldspots (i.e. hake nursery, encounter rate, trophic links

Published
2023
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10. Spatially explicit risk assessment of marine megafauna vulnerability to Indian Ocean tuna fisheries

Author

Roberson, Leslie, Wilcox, Chris, Boussarie, Germain, Dugan, Emma, Garilao, Cristina, Gonzalez, Kristofer, Green, Madeline, Kark, Salit, Kaschner, Kristin, Klein, Carissa J., Rousseau, Yannick, Vallentyne, Dan, Watson, James E. M., Kiszka, Jeremy J., Roberson, Leslie, Wilcox, Chris, Boussarie, Germain, Dugan, Emma, Garilao, Cristina, Gonzalez, Kristofer, Green, Madeline, Kark, Salit, Kaschner, Kristin, Klein, Carissa J., Rousseau, Yannick, Vallentyne, Dan, Watson, James E. M., and Kiszka, Jeremy J.

Abstract

By-catch is the most significant direct threat marine megafauna face at the global scale. However, the magnitude and spatial patterns of megafauna by-catch are still poorly understood, especially in regions with very limited monitoring and expanding fisheries. The Indian Ocean is a globally important region for megafauna biodiversity and for tuna fisheries, but has limited by-catch data. Anecdotal and scattered information indicates high by-catch could be a major threat. Here, we adapt a Productivity Susceptibility Analysis tool designed for data-poor contexts to present the first spatially explicit estimates of by-catch risk of sea turtles, elasmobranchs, and cetaceans in the three major tuna fishing gears (purse seines, longlines, and drift gill nets). Our assessment highlights a potential opportunity for multi-taxa conservation benefits by concentrating management efforts in particular coastal regions. Most coastal waters in the northern Indian Ocean, including countries that have had a minimal engagement with regional management bodies, stand out as high risk for fisheries interactions. In addition to species known to occur in tuna gears, we find high vulnerability to multiple gear types for many poorly known elasmobranchs that do not fall under any existing conservation and management measures. Our results indicate that current by-catch mitigation measures, which focus on safe-release practices, are unlikely to adequately reduce the substantial cumulative fishing impacts on vulnerable species. Preventative solutions that reduce interactions with non-target species (such as closed areas or seasons, or modifications to gear and fishing tactics) are crucial for alleviating risks to megafauna from fisheries.

Published
2022
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11. Identifying barriers to gene flow and hierarchical conservation units from seascape genomics: a modelling framework applied to a marine predator

Author

Boussarie, Germain, Momigliano, Paolo, Robbins, William D., Bonnin, Lucas, Cornu, Jean‐françois, Fauvelot, Cécile, Kiszka, Jeremy J., Manel, Stéphanie, Mouillot, David, Vigliola, Laurent, Boussarie, Germain, Momigliano, Paolo, Robbins, William D., Bonnin, Lucas, Cornu, Jean‐françois, Fauvelot, Cécile, Kiszka, Jeremy J., Manel, Stéphanie, Mouillot, David, and Vigliola, Laurent

Abstract

The ongoing decline of large marine vertebrates must be urgently mitigated, particularly under increasing levels of climate change and other anthropogenic pressures. However, characterizing the connectivity among populations remains one of the greatest challenges for the effective conservation of an increasing number of endangered species. Achieving conservation targets requires an understanding of which seascape features influence dispersal and subsequent genetic structure. This is particularly challenging for adult-disperser species, and when distribution-wide sampling is difficult. Here, we developed a two-step modelling framework to investigate how seascape features drive the genetic connectivity of marine species without larval dispersal, to better guide the design of marine protected area networks and corridors. We applied this framework to the endangered grey reef shark, Carcharhinus amblyrhynchos, a reef-associated shark distributed across the tropical Indo-Pacific. In the first step, we developed a seascape genomic approach based on isolation-by-resistance models involving circuit theory applied to 515 shark samples, genotyped for 4991 nuclear single-nucleotide polymorphisms. We show that deep oceanic areas act as strong barriers to dispersal, while proximity to habitat facilitates dispersal. In the second step, we predicted the resulting genetic differentiation across the entire distribution range of the species, providing both local and global-scale conservation units for future management guidance. We found that grey reef shark populations are more fragmented than expected for such a mobile species, raising concerns about the resilience of isolated populations under high anthropogenic pressures. We recommend the use of this framework to identify barriers to gene flow and to help in the delineation of conservation units at different scales, together with its integration across multiple species when considering marine spatial planning.

Published
2022
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12. Spatially explicit risk assessment of marine megafauna vulnerability to Indian Ocean tuna fisheries

Author

Roberson, Leslie, primary, Wilcox, Chris, additional, Boussarie, Germain, additional, Dugan, Emma, additional, Garilao, Cristina, additional, Gonzalez, Kristofer, additional, Green, Madeline, additional, Kark, Salit, additional, Kaschner, Kristin, additional, Klein, Carissa J., additional, Rousseau, Yannick, additional, Vallentyne, Dan, additional, Watson, James E. M., additional, and Kiszka, Jeremy J., additional

Published
2022
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13. Identifying barriers to gene flow and hierarchical conservation units from seascape genomics: a modelling framework applied to a marine predator

Author

Boussarie, Germain, primary, Momigliano, Paolo, additional, Robbins, William D., additional, Bonnin, Lucas, additional, Cornu, Jean‐François, additional, Fauvelot, Cécile, additional, Kiszka, Jeremy J., additional, Manel, Stéphanie, additional, Mouillot, David, additional, and Vigliola, Laurent, additional

Published
2022
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14. Identifying barriers to gene flow and hierarchical conservation units from seascape genomics: a modelling framework applied to a marine predator

Author

Boussarie, Germain, primary, Momigliano, Paolo, additional, Robbins, William D., additional, Bonnin, Lucas, additional, Cornu, Jean-François, additional, Fauvelot, Cécile, additional, Kiszka, Jeremy J., additional, Manel, Stéphanie, additional, Mouillot, David, additional, and Vigliola, Laurent, additional

Published
2021
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16. Contribution of environmental DNA analysis and seascape genomics to reef sharks conservation

Author

Boussarie, Germain, 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), Université Montpellier, David Mouillot, and Laurent Vigliola

Subjects
Récifs coralliens, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Ecologie, Coral Reefs, Sharks, Requins, ADN environnemental, Environmental DNA, Conservation, Seascape Genomics, Génomique du paysage
Abstract

Sharks represent one of the most diverse groups of predators, playing important functional roles in coastal and oceanic ecosystems. They are also one of the most threatened groups because of their vulnerability to anthropogenic pressures due to their particular life history traits. Shark populations are therefore collapsing with drastic decrease in abundance in all marine ecosystems. Even relatively common species are near- threatened. Despite the deployment of important resources for shark population assessments, 41% of the 482 shark species on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species lack a conservation status due to data deficiency. Improving our knowledge on such species is thus crucial for efficient protection to slow down their decline. More particularly, there is a necessity for a better characterization of presence, structure and connectivity of shark populations to define their conservation status, prioritize spatial management and optimize conservation efforts. This thesis relies on the emergence of new technologies to fill knowledge gaps on tropical coral reef sharks and to suggest conservation measures for better management. First, a method to survey shark communities has been developed during this thesis, based on the collection and sequencing of DNA present in the environment (environmental DNA metabarcoding; eDNA). Then, this method has been compared to exhaustive surveys of reef shark communities with traditional methods. This quick and non-invasive approach detected at least 21 shark species in waters of two distinct biogeographical areas (Caribbean and New Caledonia). Moreover, diversity and abundance patterns of DNA reads match with anthropogenic impact gradients and protected status of the sampled areas. The analysis of 22 eDNA samples detected more species in both remote reefs and impacted areas of the New Caledonian archipelago than 2758 scientific dives conducted during nearly 30 years and 385 baited remote underwater videos deployed over two years. Then, population structure and connectivity of a more common reef shark species, Carcharhinus amblyrhynchos, have been characterized using a seascape genomics approach. This thesis is based on a substantial genetic sampling in the archipelago of New Caledonia but also in several other sites in the Indo-Pacific (515 sharks in total). An isolation-by-resistance approach using circuit theory has been developed to explore what parameters are driving the genetic differentiation of C. amblyrhynchos. Here I show that deep oceanic areas act as strong barriers and proximity to habitat is a facilitator for dispersal. High-resolution modelling of genetic differentiation at the entire distribution range of the species (Indo-Pacific) led to the definition of hierarchical conservation units and a high number of isolated sites. Then, an approach taking into account the decline of abundance in impacted reefs showed an important fragmentation of shark populations and allowed the identification of remote reefs as refuges but also sources through dispersal towards impacted areas, insuring population persistence at a regional scale. This thesis demonstrates the potential of eDNA analysis for unveiling the presence of rare and elusive species such as sharks and for filling knowledge gaps in the conservation status of sharks. It also reveals the persistence of residual populations in impacted areas, that could show behavioral alterations like shifts in habitat use towards deeper waters or increased nocturnality. Finally, this thesis not only describes the population structure of a near-threatened species at high resolution and global scale, but also identifies conservation units and areas of high conservation priority that could help in the near future for the spatialization of marine management at multiple scales.; Les requins forment un des groupes de prédateurs les plus diversifiés, jouant des rôles importants au sein des écosystèmes marins. Ils forment également l’un des groupes les plus menacés car vulnérables aux pressions anthropiques du fait de leurs traits de vie particuliers. Malgré l’importance des ressources déployées pour le suivi des populations de requins, 41 % des 482 espèces recensées dans la Liste Rouge de l’UICN n’ont pas de statut de conservation par manque de données. Il devient donc primordial d’améliorer les connaissances sur ces espèces afin de les protéger et enrayer leur déclin. Il s’agit notamment de mieux caractériser la présence, la structure et la connectivité des populations de requins pour mieux définir leur statut UICN, les zones prioritaires de gestion et optimiser les efforts de conservation mis en place. Cette thèse s’appuie sur l’émergence de nouvelles technologies pour combler les lacunes de connaissances sur les requins des récifs coralliens tropicaux et proposer des actions de gestion. D’une part, une méthode d’analyse des communautés de requins par collecte et séquençage d’ADN présent dans l’environnement (métabarcoding d’ADN environnemental ; ADNe) a été développée au cours de cette thèse, puis mise en parallèle avec des suivis exhaustifs par des méthodes traditionnelles d’étude des populations de requins. Cette approche rapide et non-invasive a permis d’identifier 21 espèces de requins dans les eaux de deux domaines biogéographiques distincts (Caraïbes et Nouvelle-Calédonie). De plus, les patrons de diversité et d’abondance des fragments d’ADNe détectés coïncident avec les gradients de pression anthropique et les niveaux de protection des zones échantillonnées. L’analyse de 22 échantillons d’ADNe dans l’archipel de la Nouvelle-Calédonie a permis de déceler la présence de plus d’espèces que par 2 758 plongées scientifiques réparties sur presque 30 ans et 385 caméras appâtées déployées pendant deux ans, et ce, à la fois proche de l’homme et dans les récifs éloignés. D’autre part, la structure et connectivité des populations d’une espèce plus commune, Carcharhinus amblyrhynchos, ont été caractérisées par une approche de génomique du paysage. Cette thèse s’appuie sur un échantillonnage génétique conséquent en Nouvelle-Calédonie et dans plusieurs autres sites de l’Indo-Pacifique (515 requins). Une approche d’isolement par la résistance via la théorie des circuits a été développée afin de caractériser les paramètres influençant la dispersion de cette espèce. Ainsi, il a été montré que les zones de forte bathymétrie constituent une forte barrière à la dispersion tandis que la proximité à l’habitat récifal en est un facilitateur. La modélisation de la différenciation génétique à haute résolution et à l’échelle de l’aire de répartition de cette espèce (Indo-Pacifique) a permis de définir des unités de conservation hiérarchiques et un nombre important de sites isolés. Enfin, une approche intégrant le déclin des abondances dans les zones anthropisées a montré une fragmentation des populations de C. amblyrhynchos et a permis d’identifier certains récifs éloignés de l’homme comme refuges mais aussi sources pour un repeuplement éventuel des récifs où les populations sont menacées. Cette thèse démontre ainsi le potentiel de l’analyse de l’ADNe pour dévoiler la présence d’espèces rares et furtives telles que les requins, donnant espoir pour combler les lacunes dans leurs statuts de conservation UICN. Elle révèle également la persistance des populations résiduelles en milieu anthropisé, qui pourraient éventuellement montrer des altérations comportementales comme l’utilisation d’habitats plus profonds ou une nocturnalité plus importante. Elle décrit enfin non seulement la structure fine à grande échelle des populations d’une espèce quasi-menacée, mais identifie également des unités de conservation et des zones prioritaires à protéger pour une spatialisation des mesures de gestion à différentes échelles.

Published
2019

17. Apports de l’analyse de l’ADN environnemental et de la génomique du paysage pour la conservation des requins de récif

Author

Boussarie, Germain, 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), Université Montpellier, David Mouillot, Laurent Vigliola, and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Récifs coralliens, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Ecologie, Coral Reefs, Sharks, Requins, ADN environnemental, Environmental DNA, Conservation, Seascape Genomics, Génomique du paysage
Abstract

Sharks represent one of the most diverse groups of predators, playing important functional roles in coastal and oceanic ecosystems. They are also one of the most threatened groups because of their vulnerability to anthropogenic pressures due to their particular life history traits. Shark populations are therefore collapsing with drastic decrease in abundance in all marine ecosystems. Even relatively common species are near- threatened. Despite the deployment of important resources for shark population assessments, 41% of the 482 shark species on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species lack a conservation status due to data deficiency. Improving our knowledge on such species is thus crucial for efficient protection to slow down their decline. More particularly, there is a necessity for a better characterization of presence, structure and connectivity of shark populations to define their conservation status, prioritize spatial management and optimize conservation efforts. This thesis relies on the emergence of new technologies to fill knowledge gaps on tropical coral reef sharks and to suggest conservation measures for better management. First, a method to survey shark communities has been developed during this thesis, based on the collection and sequencing of DNA present in the environment (environmental DNA metabarcoding; eDNA). Then, this method has been compared to exhaustive surveys of reef shark communities with traditional methods. This quick and non-invasive approach detected at least 21 shark species in waters of two distinct biogeographical areas (Caribbean and New Caledonia). Moreover, diversity and abundance patterns of DNA reads match with anthropogenic impact gradients and protected status of the sampled areas. The analysis of 22 eDNA samples detected more species in both remote reefs and impacted areas of the New Caledonian archipelago than 2758 scientific dives conducted during nearly 30 years and 385 baited remote underwater videos deployed over two years. Then, population structure and connectivity of a more common reef shark species, Carcharhinus amblyrhynchos, have been characterized using a seascape genomics approach. This thesis is based on a substantial genetic sampling in the archipelago of New Caledonia but also in several other sites in the Indo-Pacific (515 sharks in total). An isolation-by-resistance approach using circuit theory has been developed to explore what parameters are driving the genetic differentiation of C. amblyrhynchos. Here I show that deep oceanic areas act as strong barriers and proximity to habitat is a facilitator for dispersal. High-resolution modelling of genetic differentiation at the entire distribution range of the species (Indo-Pacific) led to the definition of hierarchical conservation units and a high number of isolated sites. Then, an approach taking into account the decline of abundance in impacted reefs showed an important fragmentation of shark populations and allowed the identification of remote reefs as refuges but also sources through dispersal towards impacted areas, insuring population persistence at a regional scale. This thesis demonstrates the potential of eDNA analysis for unveiling the presence of rare and elusive species such as sharks and for filling knowledge gaps in the conservation status of sharks. It also reveals the persistence of residual populations in impacted areas, that could show behavioral alterations like shifts in habitat use towards deeper waters or increased nocturnality. Finally, this thesis not only describes the population structure of a near-threatened species at high resolution and global scale, but also identifies conservation units and areas of high conservation priority that could help in the near future for the spatialization of marine management at multiple scales.; Les requins forment un des groupes de prédateurs les plus diversifiés, jouant des rôles importants au sein des écosystèmes marins. Ils forment également l’un des groupes les plus menacés car vulnérables aux pressions anthropiques du fait de leurs traits de vie particuliers. Malgré l’importance des ressources déployées pour le suivi des populations de requins, 41 % des 482 espèces recensées dans la Liste Rouge de l’UICN n’ont pas de statut de conservation par manque de données. Il devient donc primordial d’améliorer les connaissances sur ces espèces afin de les protéger et enrayer leur déclin. Il s’agit notamment de mieux caractériser la présence, la structure et la connectivité des populations de requins pour mieux définir leur statut UICN, les zones prioritaires de gestion et optimiser les efforts de conservation mis en place. Cette thèse s’appuie sur l’émergence de nouvelles technologies pour combler les lacunes de connaissances sur les requins des récifs coralliens tropicaux et proposer des actions de gestion. D’une part, une méthode d’analyse des communautés de requins par collecte et séquençage d’ADN présent dans l’environnement (métabarcoding d’ADN environnemental ; ADNe) a été développée au cours de cette thèse, puis mise en parallèle avec des suivis exhaustifs par des méthodes traditionnelles d’étude des populations de requins. Cette approche rapide et non-invasive a permis d’identifier 21 espèces de requins dans les eaux de deux domaines biogéographiques distincts (Caraïbes et Nouvelle-Calédonie). De plus, les patrons de diversité et d’abondance des fragments d’ADNe détectés coïncident avec les gradients de pression anthropique et les niveaux de protection des zones échantillonnées. L’analyse de 22 échantillons d’ADNe dans l’archipel de la Nouvelle-Calédonie a permis de déceler la présence de plus d’espèces que par 2 758 plongées scientifiques réparties sur presque 30 ans et 385 caméras appâtées déployées pendant deux ans, et ce, à la fois proche de l’homme et dans les récifs éloignés. D’autre part, la structure et connectivité des populations d’une espèce plus commune, Carcharhinus amblyrhynchos, ont été caractérisées par une approche de génomique du paysage. Cette thèse s’appuie sur un échantillonnage génétique conséquent en Nouvelle-Calédonie et dans plusieurs autres sites de l’Indo-Pacifique (515 requins). Une approche d’isolement par la résistance via la théorie des circuits a été développée afin de caractériser les paramètres influençant la dispersion de cette espèce. Ainsi, il a été montré que les zones de forte bathymétrie constituent une forte barrière à la dispersion tandis que la proximité à l’habitat récifal en est un facilitateur. La modélisation de la différenciation génétique à haute résolution et à l’échelle de l’aire de répartition de cette espèce (Indo-Pacifique) a permis de définir des unités de conservation hiérarchiques et un nombre important de sites isolés. Enfin, une approche intégrant le déclin des abondances dans les zones anthropisées a montré une fragmentation des populations de C. amblyrhynchos et a permis d’identifier certains récifs éloignés de l’homme comme refuges mais aussi sources pour un repeuplement éventuel des récifs où les populations sont menacées. Cette thèse démontre ainsi le potentiel de l’analyse de l’ADNe pour dévoiler la présence d’espèces rares et furtives telles que les requins, donnant espoir pour combler les lacunes dans leurs statuts de conservation UICN. Elle révèle également la persistance des populations résiduelles en milieu anthropisé, qui pourraient éventuellement montrer des altérations comportementales comme l’utilisation d’habitats plus profonds ou une nocturnalité plus importante. Elle décrit enfin non seulement la structure fine à grande échelle des populations d’une espèce quasi-menacée, mais identifie également des unités de conservation et des zones prioritaires à protéger pour une spatialisation des mesures de gestion à différentes échelles.

Published
2019

18. Remote reefs and seamounts are the last refuges for marine predators across the Indo-Pacific

Author

Letessier, Tom B., Mouillot, David, Bouchet, Phil J., Vigliola, Laurent, Fernandes, Marjorie C., Thompson, Chris, Boussarie, Germain, Turner, Jemma, Juhel, Jean-baptiste, Maire, Eva, Caley, M. Julian, Koldewey, Heather J., Friedlander, Alan, Sala, Enric, Meeuwig, Jessica J., Letessier, Tom B., Mouillot, David, Bouchet, Phil J., Vigliola, Laurent, Fernandes, Marjorie C., Thompson, Chris, Boussarie, Germain, Turner, Jemma, Juhel, Jean-baptiste, Maire, Eva, Caley, M. Julian, Koldewey, Heather J., Friedlander, Alan, Sala, Enric, and Meeuwig, Jessica J.

Abstract

Since the 1950s, industrial fisheries have expanded globally, as fishing vessels are required to travel further afield for fishing opportunities. Technological advancements and fishery subsidies have granted ever-increasing access to populations of sharks, tunas, billfishes, and other predators. Wilderness refuges, defined here as areas beyond the detectable range of human influence, are therefore increasingly rare. In order to achieve marine resources sustainability, large no-take marine protected areas (MPAs) with pelagic components are being implemented. However, such conservation efforts require knowledge of the critical habitats for predators, both across shallow reefs and the deeper ocean. Here, we fill this gap in knowledge across the Indo-Pacific by using 1,041 midwater baited videos to survey sharks and other pelagic predators such as rainbow runner (Elagatis bipinnulata), mahi-mahi (Coryphaena hippurus), and black marlin (Istiompax indica). We modeled three key predator community attributes: vertebrate species richness, mean maximum body size, and shark abundance as a function of geomorphology, environmental conditions, and human pressures. All attributes were primarily driven by geomorphology (35%−62% variance explained) and environmental conditions (14%−49%). While human pressures had no influence on species richness, both body size and shark abundance responded strongly to distance to human markets (12%−20%). Refuges were identified at more than 1,250 km from human markets for body size and for shark abundance. These refuges were identified as remote and shallow seabed features, such as seamounts, submerged banks, and reefs. Worryingly, hotpots of large individuals and of shark abundance are presently under-represented within no-take MPAs that aim to effectively protect marine predators, such as the British Indian Ocean Territory. Population recovery of predators is unlikely to occur without strategic placement and effective enforcement of large no-take

Published
2019
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19. Correction:Remote reefs and seamounts are the last refuges for marine predators across the Indo-Pacific (PLoS Biology (2019) 17:8 (e3000366) DOI: 10.1371/journal.pbio.3000366)

Author

Letessier, Tom B., Mouillot, David, Bouchet, Phil J., Vigliola, Laurent, Fernandes, Marjorie C., Thompson, Chris, Boussarie, Germain, Turner, Jemma, Juhel, Jean Baptiste, Maire, Eva, Julian Caley, M., Koldewey, Heather J., Friedlander, Alan, Sala, Enric, Meeuwig, Jessica J., Letessier, Tom B., Mouillot, David, Bouchet, Phil J., Vigliola, Laurent, Fernandes, Marjorie C., Thompson, Chris, Boussarie, Germain, Turner, Jemma, Juhel, Jean Baptiste, Maire, Eva, Julian Caley, M., Koldewey, Heather J., Friedlander, Alan, Sala, Enric, and Meeuwig, Jessica J.

Abstract

There are two textual errors in the published paper. In the Abstract, the last line reads “hotpots” instead of “hotspots.” The same textual error is present in the Introduction. The last line of the Abstract should read as follows: Worryingly, hotspots of large individuals and of shark abundance are presently under-represented within no-take MPAs that aim to effectively protect marine predators, such as the British Indian Ocean Territory. Population recovery of predators is unlikely to occur without strategic placement and effective enforcement of large no-take MPAs in both coastal and remote locations. The first line of the last paragraph of the Introduction should read as follows: Here, we utilize an extensive data set of standardized and nondestructive baited video surveys from nine regions across the Indo-Pacific region to model predator diversity and abundance and to identify hotspots of vertebrate species richness, mean maximum body size weighted by abundance (hereafter “body size”), and shark abundance as a function of environmental conditions, geomorphology, human pressure, and management levels. The funding statement also ommits funding received from the Centre for the Synthesis and Analysis of Biodiversity. The amended Financial Disclosure should read as follows: This work was supported by the Australian Government’s National Environmental Research Program (NERP) Marine Biodiversity Hub (TBL, PB, JC, JJM) and by the Bertar-elli Foundation (TBL, JJM). Additional support was provided by Darwin Initiative grant (Project #19027, HK), Centre for the Synthesis and Analysis of Biodiversity (CESAB, TBL, DM, LV, JBJ, JJM), Total Foundation (PELAGIC Project, TBL, DM, LV, JBJ, JJM), French Oceanic Fleet and New Caledonian Government Pristine reef and Apex grants (DM, LV), and National Geographic’s Pristine Seas programme (AF, ES).’

Published
2019

20. Correction: Remote reefs and seamounts are the last refuges for marine predators across the Indo-Pacific

Author

Letessier, Tom B., primary, Mouillot, David, additional, Bouchet, Phil J., additional, Vigliola, Laurent, additional, Fernandes, Marjorie C., additional, Thompson, Chris, additional, Boussarie, Germain, additional, Turner, Jemma, additional, Juhel, Jean-Baptiste, additional, Maire, Eva, additional, Caley, M. Julian, additional, Koldewey, Heather J., additional, Friedlander, Alan, additional, Sala, Enric, additional, and Meeuwig, Jessica J., additional

Published
2019
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21. Remote reefs and seamounts are the last refuges for marine predators across the Indo-Pacific

Author

Letessier, Tom B., primary, Mouillot, David, additional, Bouchet, Phil J., additional, Vigliola, Laurent, additional, Fernandes, Marjorie C., additional, Thompson, Chris, additional, Boussarie, Germain, additional, Turner, Jemma, additional, Juhel, Jean-Baptiste, additional, Maire, Eva, additional, Caley, M. Julian, additional, Koldewey, Heather J., additional, Friedlander, Alan, additional, Sala, Enric, additional, and Meeuwig, Jessica J., additional

Published
2019
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22. Environmental DNA illuminates the dark diversity of sharks

Author

Boussarie, Germain, Bakker, Judith, Wangensteen, Owen S., Mariani, Stefano, Bonnin, Lucas, Juhel, Jean-baptiste, Kiszka, Jeremy J., Kulbicki, Michel, Manel, Stephanie, Robbins, William D., Vigliola, Laurent, Mouillot, David, Boussarie, Germain, Bakker, Judith, Wangensteen, Owen S., Mariani, Stefano, Bonnin, Lucas, Juhel, Jean-baptiste, Kiszka, Jeremy J., Kulbicki, Michel, Manel, Stephanie, Robbins, William D., Vigliola, Laurent, and Mouillot, David

Abstract

In the era of "Anthropocene defaunation," large species are often no longer detected in habitats where they formerly occurred. However, it is unclear whether this apparent missing, or "dark," diversity of megafauna results from local species extirpations or from failure to detect elusive remaining individuals. We find that despite two orders of magnitude less sampling effort, environmental DNA (eDNA) detects 44% more shark species than traditional underwater visual censuses and baited videos across the New Caledonian archipelago (south-western Pacific). Furthermore, eDNA analysis reveals the presence of previously unobserved shark species in human-impacted areas. Overall, our results highlight a greater prevalence of sharks than described by traditional survey methods in both impacted and wilderness areas. This indicates an urgent need for large-scale eDNA assessments to improve monitoring of threatened and elusive megafauna. Finally, our findings emphasize the need for conservation efforts specifically geared toward the protection of elusive, residual populations.

Published
2018
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23. Seabirds supply nitrogen to reefbuilding corals on remote Pacific islets

Author

Lorrain, Anne, Houlbreque, Fanny, Benzoni, Francesca, Barjon, Lucie, Tremblay-Boyer, Laura, Menkès, Christophe E., Gillikin, David P., Payri, Claude, Jourdan, Herve, Boussarie, Germain, Verheyden, Anouk, Vidal, Eric, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), 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), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Pacific community (SPC), Processus de couplage à Petite Echelle, Ecosystèmes et Prédateurs Supérieurs (PEPS), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Union College, 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), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), 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)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Université de la Nouvelle-Calédonie (UNC), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD)

Subjects
STYLOPHORA-PISTILLATA, GREAT-BARRIER-REEF, ACL, fungi, OCEAN ACIDIFICATION, technology, industry, and agriculture, biochemical phenomena, metabolism, and nutrition, SKELETAL GROWTH, NEW-CALEDONIA, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, WATER-QUALITY, population characteristics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ISLANDS, MARINE, geographic locations, SCLERACTINIAN CORALS, NITRATE
Abstract

International audience; Seabirds concentrate nutrients from large marine areas on their nesting islands playing an important ecological role in nutrient transfer between marine and terrestrial ecosystems. Here we investigate the role of guano on corals reefs across scales by analyzing the stable nitrogen isotopic (δ15N) values of the scleractinian coral Pocillopora damicornis on fringing reefs around two Pacific remote islets with large seabird colonies. Marine stations closest to the seabird colonies had higher nitrate + nitrite concentrations compared to more distant stations. Coral and zooxanthellae δ15N values were also higher at these sites, suggesting that guano-derived nitrogen is assimilated into corals and contributes to their nitrogen requirements. The spatial extent of guano influence was however restricted to a local scale. Our results demonstrate that seabird-derived nutrients not only spread across the terrestrial ecosystem, but also affect components of the adjacent marine ecosystem. Further studies are now needed to assess if this nutrient input has a positive or negative effect for corals. Such studies on remote islets also open fresh perspectives to understand how nutrients affect coral reefs isolated from other anthropogenic stressors.

Published
2017
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24. Seabirds supply nitrogen to reef-building corals on remote Pacific islets

Author

Lorrain, Anne, Houlbrèque, Fanny, Benzoni, Francesca, Barjon, Lucie, Tremblay-Boyer, Laura, Menkes, Christophe, Gillikin, David P., Payri, Claude, Jourdan, Hervé, Boussarie, Germain, Verheyden, Anouk, Vidal, Eric, Lorrain, A, Houlbrèque, F, Benzoni, F, Barjon, L, Tremblay-Boyer, L, Menkes, C, Gillikin, D, Payri, C, Jourdan, H, Boussarie, G, Verheyden, A, and Vidal, E

Subjects
Food Chain, Pacific Ocean, Multidisciplinary, Coral Reefs, Nitrogen, Science, fungi, technology, industry, and agriculture, Nutrients, biochemical phenomena, metabolism, and nutrition, Anthozoa, Article, Birds, Isotopes, Animals, population characteristics, Medicine, Ecosystem, geographic locations, BIO/05 - ZOOLOGIA
Abstract

Seabirds concentrate nutrients from large marine areas on their nesting islands playing an important ecological role in nutrient transfer between marine and terrestrial ecosystems. Here we investigate the role of guano on corals reefs across scales by analyzing the stable nitrogen isotopic (δ15N) values of the scleractinian coral Pocillopora damicornis on fringing reefs around two Pacific remote islets with large seabird colonies. Marine stations closest to the seabird colonies had higher nitrate + nitrite concentrations compared to more distant stations. Coral and zooxanthellae δ15N values were also higher at these sites, suggesting that guano-derived nitrogen is assimilated into corals and contributes to their nitrogen requirements. The spatial extent of guano influence was however restricted to a local scale. Our results demonstrate that seabird-derived nutrients not only spread across the terrestrial ecosystem, but also affect components of the adjacent marine ecosystem. Further studies are now needed to assess if this nutrient input has a positive or negative effect for corals. Such studies on remote islets also open fresh perspectives to understand how nutrients affect coral reefs isolated from other anthropogenic stressors.

Published
2017

25. Environmental DNA illuminates the dark diversity of sharks

Author

Boussarie, Germain, primary, Bakker, Judith, additional, Wangensteen, Owen S., additional, Mariani, Stefano, additional, Bonnin, Lucas, additional, Juhel, Jean-Baptiste, additional, Kiszka, Jeremy J., additional, Kulbicki, Michel, additional, Manel, Stephanie, additional, Robbins, William D., additional, Vigliola, Laurent, additional, and Mouillot, David, additional

Published
2018
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26. Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact

Author

Bakker, Judith, Wangensteen, Owen S., Chapman, Demian D., Boussarie, Germain, Buddo, Dayne, Guttridge, Tristan L., Hertler, Heidi, Mouillot, David, Vigliola, Laurent, Mariani, Stefano, Bakker, Judith, Wangensteen, Owen S., Chapman, Demian D., Boussarie, Germain, Buddo, Dayne, Guttridge, Tristan L., Hertler, Heidi, Mouillot, David, Vigliola, Laurent, and Mariani, Stefano

Abstract

Sharks are charismatic predators that play a key role in most marine food webs. Their demonstrated vulnerability to exploitation has recently turned them into flagship species in ocean conservation. Yet, the assessment and monitoring of the distribution and abundance of such mobile species in marine environments remain challenging, often invasive and resource-intensive. Here we pilot a novel, rapid and non-invasive environmental DNA (eDNA) metabarcoding approach specifically targeted to infer shark presence, diversity and eDNA read abundance in tropical habitats. We identified at least 21 shark species, from both Caribbean and Pacific Coral Sea water samples, whose geographical patterns of diversity and read abundance coincide with geographical differences in levels of anthropogenic pressure and conservation effort. We demonstrate that eDNA metabarcoding can be effectively employed to study shark diversity. Further developments in this field have the potential to drastically enhance our ability to assess and monitor elusive oceanic predators, and lead to improved conservation strategies.

Published
2017
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28. Seabirds supply nitrogen to reef-building corals on remote Pacific islets

Author

Lorrain, Anne, primary, Houlbrèque, Fanny, additional, Benzoni, Francesca, additional, Barjon, Lucie, additional, Tremblay-Boyer, Laura, additional, Menkes, Christophe, additional, Gillikin, David P., additional, Payri, Claude, additional, Jourdan, Hervé, additional, Boussarie, Germain, additional, Verheyden, Anouk, additional, and Vidal, Eric, additional

Published
2017
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