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5. A global database for metacommunity ecology, integrating species, traits, environment and space

Author

Jeliazkov, Alienor, Mijatovic, Darko, Chantepie, Stéphane, Andrew, Nigel, Arlettaz, Raphaël, Barbaro, Luc, Barsoum, Nadia, Bartonova, Alena, Belskaya, Elena, Bonada, Núria, Brind’Amour, Anik, Carvalho, Rodrigo, Castro, Helena, Chmura, Damian, Choler, Philippe, Chong-Seng, Karen, Cleary, Daniel, Cormont, Anouk, Cornwell, William, de Campos, Ramiro, de Voogd, Nicole, Doledec, Sylvain, Drew, Joshua, Dziock, Frank, Eallonardo, Anthony, Edgar, Melanie J, Farneda, Fábio, Hernandez, Domingo Flores, Frenette-Dussault, Cédric, Fried, Guillaume, Gallardo, Belinda, Gibb, Heloise, Gonçalves-Souza, Thiago, Higuti, Janet, Humbert, Jean-Yves, Krasnov, Boris R, Saux, Eric Le, Lindo, Zoe, Lopez-Baucells, Adria, Lowe, Elizabeth, Marteinsdottir, Bryndis, Martens, Koen, Meffert, Peter, Mellado-Díaz, Andres, Menz, Myles HM, Meyer, Christoph FJ, Miranda, Julia Ramos, Mouillot, David, Ossola, Alessandro, Pakeman, Robin, Pavoine, Sandrine, Pekin, Burak, Pino, Joan, Pocheville, Arnaud, Pomati, Francesco, Poschlod, Peter, Prentice, Honor C, Purschke, Oliver, Raevel, Valerie, Reitalu, Triin, Renema, Willem, Ribera, Ignacio, Robinson, Natalie, Robroek, Bjorn, Rocha, Ricardo, Shieh, Sen-Her, Spake, Rebecca, Staniaszek-Kik, Monika, Stanko, Michal, Tejerina-Garro, Francisco Leonardo, Braak, Cajo ter, Urban, Mark C, Klink, Roel van, Villéger, Sébastien, Wegman, Ruut, Westgate, Martin J, Wolff, Jonas, Żarnowiec, Jan, Zolotarev, Maxim, and Chase, Jonathan M

Subjects
Climate Change Impacts and Adaptation, Ecological Applications, Biological Sciences, Ecology, Environmental Sciences, Life on Land, Animals, Biodiversity, Biota, Plants
Abstract

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; "CESTES". Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.

Published
2020

6. Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space

Author

Jeliazkov, Alienor, Mijatovic, Darko, Chantepie, Stéphane, Andrew, Nigel, Arlettaz, Raphaël, Barbaro, Luc, Barsoum, Nadia, Bartonova, Alena, Belskaya, Elena, Bonada, Núria, Brind’Amour, Anik, Carvalho, Rodrigo, Castro, Helena, Chmura, Damian, Choler, Philippe, Chong-Seng, Karen, Cleary, Daniel, Cormont, Anouk, Cornwell, William, de Campos, Ramiro, de Voogd, Nicole, Doledec, Sylvain, Drew, Joshua, Dziock, Frank, Eallonardo, Anthony, Edgar, Melanie J, Farneda, Fábio, Hernandez, Domingo Flores, Frenette-Dussault, Cédric, Fried, Guillaume, Gallardo, Belinda, Gibb, Heloise, Gonçalves-Souza, Thiago, Higuti, Janet, Humbert, Jean-Yves, Krasnov, Boris R, Saux, Eric Le, Lindo, Zoe, Lopez-Baucells, Adria, Lowe, Elizabeth, Marteinsdottir, Bryndis, Martens, Koen, Meffert, Peter, Mellado-Díaz, Andres, Menz, Myles HM, Meyer, Christoph FJ, Miranda, Julia Ramos, Mouillot, David, Ossola, Alessandro, Pakeman, Robin, Pavoine, Sandrine, Pekin, Burak, Pino, Joan, Pocheville, Arnaud, Pomati, Francesco, Poschlod, Peter, Prentice, Honor C, Purschke, Oliver, Raevel, Valerie, Reitalu, Triin, Renema, Willem, Ribera, Ignacio, Robinson, Natalie, Robroek, Bjorn, Rocha, Ricardo, Shieh, Sen-Her, Spake, Rebecca, Staniaszek-Kik, Monika, Stanko, Michal, Tejerina-Garro, Francisco Leonardo, Braak, Cajo ter, Urban, Mark C, Klink, Roel van, Villéger, Sébastien, Wegman, Ruut, Westgate, Martin J, Wolff, Jonas, Żarnowiec, Jan, Zolotarev, Maxim, and Chase, Jonathan M

Subjects
Environmental Sciences, Biological Sciences, Ecology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

7. Biological trade-offs underpin coral reef ecosystem functioning

Author

Schiettekatte, Nina M. D., Brandl, Simon J., Casey, Jordan M., Graham, Nicholas A. J., Barneche, Diego R., Burkepile, Deron E., Allgeier, Jacob E., Arias-Gonzaléz, Jesús E., Edgar, Graham J., Ferreira, Carlos E. L., Floeter, Sergio R., Friedlander, Alan M., Green, Alison L., Kulbicki, Michel, Letourneur, Yves, Luiz, Osmar J., Mercière, Alexandre, Morat, Fabien, Munsterman, Katrina S., Rezende, Enrico L., Rodríguez‐Zaragoza, Fabian A., Stuart-Smith, Rick D., Vigliola, Laurent, Villéger, Sébastien, and Parravicini, Valeriano

Published
2022
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10. Inferring the extinction risk of marine fish to inform global conservation priorities.

Author

Loiseau, Nicolas, Mouillot, David, Velez, Laure, Seguin, Raphaël, Casajus, Nicolas, Coux, Camille, Albouy, Camille, Claverie, Thomas, Duhamet, Agnès, Fleure, Valentine, Langlois, Juliette, Villéger, Sébastien, and Mouquet, Nicolas

Subjects
MARINE fishes, ENDANGERED species, BIOLOGICAL extinction, NATURE conservation, MARINE parks & reserves
Abstract

While extinction risk categorization is fundamental for building robust conservation planning for marine fishes, empirical data on occurrence and vulnerability to disturbances are still lacking for most marine teleost fish species, preventing the assessment of their International Union for the Conservation of Nature (IUCN) status. In this article, we predicted the IUCN status of marine fishes based on two machine learning algorithms, trained with available species occurrences, biological traits, taxonomy, and human uses. We found that extinction risk for marine fish species is higher than initially estimated by the IUCN, increasing from 2.5% to 12.7%. Species predicted as Threatened were mainly characterized by a small geographic range, a relatively large body size, and a low growth rate. Hotspots of predicted Threatened species peaked mainly in the South China Sea, the Philippine Sea, the Celebes Sea, the west coast Australia and North America. We also explored the consequences of including these predicted species' IUCN status in the prioritization of marine protected areas through conservation planning. We found a marked increase in prioritization ranks for subpolar and polar regions despite their low species richness. We suggest to integrate multifactorial ensemble learning to assess species extinction risk and offer a more complete view of endangered taxonomic groups to ultimately reach global conservation targets like the extending coverage of protected areas where species are the most vulnerable. Empirical data on occurrences and vulnerability are still lacking for most marine teleost fish species, preventing assessment of their IUCN extinction risk status. This study uses machine learning with occurrence data, species biological traits, taxonomy and human usage to infer a 12.8% extinction risk for marine fish species, surpassing existing estimates. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Fish communities can simultaneously contribute to nature and people across the world’s tropical reefs

Author

Flandrin, Ulysse, Mouillot, David, Albouy, Camille, Bejarano, Sonia, Casajus, Nicolas, Cinner, Joshua, Edgar, Graham, Ghilardi, Mattia, Leprieur, Fabien, Loiseau, Nicolas, MacNeil, Aaron, Maire, Eva, McLean, Matthew, Parravicini, Valeriano, Pellissier, Loïc, Schiettekatte, Nina, Stuart-Smith, Rick D., Villéger, Sébastien, and Mouquet, Nicolas

Abstract

Anthropogenic activities are eroding biodiversity and its contributions to nature and people worldwide. Yet, the dual imperative to protect nature and sustain human well-being raises potential trade-offs that remain to be quantified. Using standardized fish surveys across 1,237 tropical reefs worldwide, we converted the presence and abundance data of 1,024 species into 29 fish community contributions that primarily benefit either nature or people. We show that “nature-for-nature” contributions are mostly positively correlated with total fish biomass, while “nature-for-people” contributions are more independent. Trade-offs among contributions are not the rule, with some tropical fish communities simultaneously providing high levels of different contributions. High mean contributions have been found in all tropical oceans, so sustaining healthy tropical reefs while promoting human well-being seems achievable within most countries, rather than mutually exclusive. Our framework offers an opportunity to explore different management strategies and pathways on tropical reefs between the use and the sparing of nature toward more favorable and sustainable ecological and social futures.

Published
2024
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15. Functional changes across marine habitats due to ocean acidification

Author

Teixidó, Núria, Carlot, Jérémy, Alliouane, Samir, Ballesteros, Enric, De vittor, Cinzia, Gambi, Maria Cristina, Gattuso, Jean‐pierre, Kroeker, Kristy, Micheli, Fiorenza, Mirasole, Alice, Parravacini, Valeriano, Villéger, Sébastien, Teixidó, Núria, Carlot, Jérémy, Alliouane, Samir, Ballesteros, Enric, De vittor, Cinzia, Gambi, Maria Cristina, Gattuso, Jean‐pierre, Kroeker, Kristy, Micheli, Fiorenza, Mirasole, Alice, Parravacini, Valeriano, and Villéger, Sébastien

Abstract

Global environmental change drives diversity loss and shifts in community structure. A key challenge is to better understand the impacts on ecosystem function and to connect species and trait diversity of assemblages with ecosystem properties that are in turn linked to ecosystem functioning. Here we quantify shifts in species composition and trait diversity associated with ocean acidification (OA) by using field measurements at marine CO2 vent systems spanning four reef habitats across different depths in a temperate coastal ecosystem. We find that both species and trait diversity decreased, and that ecosystem properties (understood as the interplay between species, traits, and ecosystem function) shifted with acidification. Furthermore, shifts in trait categories such as autotrophs, filter feeders, herbivores, and habitat‐forming species were habitat‐specific, indicating that OA may produce divergent responses across habitats and depths. Combined, these findings reveal the importance of connecting species and trait diversity of marine benthic habitats with key ecosystem properties to anticipate the impacts of global environmental change. Our results also generate new insights on the predicted general and habitat‐specific ecological consequences of OA.

Published
2024
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16. Automated identification of invasive rabbitfishes in underwater images from the Mediterranean Sea

Author

Fleuré, Valentine, Magneville, Camille, Mouillot, David, Villéger, Sébastien, Fleuré, Valentine, Magneville, Camille, Mouillot, David, and Villéger, Sébastien

Abstract

Coastal ecosystems of the Mediterranean Sea are among the richest in non-indigenous species, mostly due to the establishment of species coming from the Red Sea through the Suez Canal. Two herbivorous rabbitfishes, Siganus rivulatus and Siganus luridus, are already invasive in the south-eastern part of the Mediterranean Sea where they cause ecological damage by overgrazing algae. The early detection and the counting of these non-indigenous species in the rest of the Mediterranean Sea is thus a major challenge for scientists and ecosystem managers. However, analysing images from divers or remote cameras is a demanding task. Here, a dataset of 31,285 images of Siganus spp. and of six common native fishes to the Mediterranean Sea was built from 40 underwater videos recorded at three reef habitats. A deep learning algorithm was then trained to identify Siganus spp. on images containing the eight Mediterranean species. Finally, the algorithm and a post-processing filtering were tested with an independent dataset of 2024 images. The model had a recall of 0.92 for the Siganus genus (i.e., two Siganus species combined). After a confidence-based post-processing, the recall increased to 0.98 with only 4 out of 272 images of Siganus spp. being misclassified. Accuracy reached a score of 0.61 meaning that experts would have to discard false positives. Images of five native species not present in the training dataset yielded similar false positive rates than species present in the training dataset. Overall, the automatic processing of images by the model and then the checking of putative Siganus images by experts required up to five times less effort than a full processing by experts. The algorithm can help to efficiently detect these two invasive fishes in underwater images to evaluate progress towards conservation objectives and accelerate citizen-based monitoring of coastal ecosystems.

Published
2024
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18. Functional changes across marine habitats due to ocean acidification

Author

Teixidó, Núria, primary, Carlot, Jérémy, additional, Alliouane, Samir, additional, Ballesteros, Enric, additional, De Vittor, Cinzia, additional, Gambi, Maria Cristina, additional, Gattuso, Jean‐Pierre, additional, Kroeker, Kristy, additional, Micheli, Fiorenza, additional, Mirasole, Alice, additional, Parravacini, Valeriano, additional, and Villéger, Sébastien, additional

Published
2024
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25. Formal Method for Mission Controller Generation of a Mobile Robot

Author

Louis, Silvain, Godary-Dejean, Karen, Lapierre, Lionel, Claverie, Thomas, Villéger, Sébastien, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Gao, Yang, editor, Fallah, Saber, editor, Jin, Yaochu, editor, and Lekakou, Constantina, editor

Published
2017
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27. A global database of nitrogen and phosphorus excretion rates of aquatic animals

Author

Vanni, Michael J., McIntyre, Peter B., Allen, Dennis, Arnott, Diane L., Benstead, Jonathan P., Berg, David J., Brabrand, Åge, Brosse, Sébastien, Bukaveckas, Paul A., Caliman, Adriano, Capps, Krista A., Carneiro, Luciana S., Chadwick, Nanette E., Christian, Alan D., Clarke, Andrew, Conroy, Joseph D., Cross, Wyatt F., Culver, David A., Dalton, Christopher M., Devine, Jennifer A., Domine, Leah M., Evans-White, Michelle A., Faafeng, Bjørn A., Flecker, Alexander S., Gido, Keith B., Godinot, Claire, Guariento, Rafael D., Haertel-Borer, Susanne, Hall, Robert O., Henry, Raoul, Herwig, Brian R., Hicks, Brendan J., Higgins, Karen A., Hood, James M., Hopton, Matthew E., Ikeda, Tsutomu, James, William F., Jansen, Henrice M., Johnson, Cody R., Koch, Benjamin J., Lamberti, Gary A., Lessard-Pilon, Stephanie, Maerz, John C., Mather, Martha E., McManamay, Ryan A., Milanovich, Joseph R., Morgan, Dai K. J., Moslemi, Jennifer M., Naddafi, Rahmat, Nilssen, Jens Petter, Pagano, Marc, Pilati, Alberto, Post, David M., Roopin, Modi, Rugenski, Amanda T., Schaus, Maynard H., Shostell, Joseph, Small, Gaston E., Solomon, Christopher T., Sterrett, Sean C., Strand, Øivind, Tarvainen, Marjo, Taylor, Jason M., Torres-Gerald, Lisette E., Turner, Caroline B., Urabe, Jotaro, Uye, Shin-Ichi, Ventelä, Anne-Mari, Villeger, Sébastien, Whiles, Matt R., Wilhelm, Frank M., Wilson, Henry F., Xenopoulos, Marguerite A., and Zimmer, Kyle D.

Published
2017

28. Coral Reef Fish Detection and Recognition in Underwater Videos by Supervised Machine Learning: Comparison Between Deep Learning and HOG+SVM Methods

Author

Villon, Sébastien, Chaumont, Marc, Subsol, Gérard, Villéger, Sébastien, Claverie, Thomas, Mouillot, David, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Blanc-Talon, Jacques, editor, Distante, Cosimo, editor, Philips, Wilfried, editor, Popescu, Dan, editor, and Scheunders, Paul, editor

Published
2016
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32. Stocking practices shape the taxonomic and functional diversity of fish communities in gravel pit lakes.

Author

Gimenez, Marie, Villéger, Sébastien, Grenouillet, Gaël, and Cucherousset, Julien

Subjects
*FISH communities, *FISH diversity, *FISHING villages, *GRAVEL, *ECOSYSTEM dynamics
Abstract

Freshwater fishes are widely stocked to enhance existing stocks and create new fishery opportunities, but quantification of ecological effects of stocking on recipient communities is still limited. Here, we quantified recent stocking practices in geographically close gravel pit lakes with contrasting history and management, and measured effects of stocking on fish community structure (taxonomic and functional diversity and body‐size structure). Between 2011 and 2017, 50% of managers stocked fish into gravel pit lakes at least once. However, stocking density (1.6 kg.year−1.ha−1 to 907 kg.year−1.ha−1), stocking diversity, and species stocked (from rainbow trout‐dominated to cyprinid‐dominated) were highly variable. Stocking intensity and choice of stocked species were primarily driven by management objectives and lake size. Stocking intensity was associated with changes in the recipient fish community, with an increase in taxonomic and functional richness and nonlinear changes in community size spectrum. Our findings demonstrate that recent stocking practices can modulate ecological dynamics of fish communities in gravel pit lakes with important consequences on functional characteristics that should be incorporated into management practices. [ABSTRACT FROM AUTHOR]

Published
2023
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34. Inferring functional diversity from environmental DNA metabarcoding

Author

Condachou, Céline, Milhau, Tristan, Murienne, Jérôme, Brosse, Sébastien, Villéger, Sébastien, Valentini, Alice, Dejean, Tony, Mouillot, David, Condachou, Céline, Milhau, Tristan, Murienne, Jérôme, Brosse, Sébastien, Villéger, Sébastien, Valentini, Alice, Dejean, Tony, and Mouillot, David

Abstract

Environmental DNA (eDNA) metabarcoding is a reliable method to assess taxonomic diversity, but the incompleteness of genetic reference databases prevents the assignation of many sequences to a given species. Functional diversity (FD) is a key biodiversity facet to monitor, but it requires the identification of all species within communities to account for their trait values. So, the ability of eDNA-based inventories to estimate the “true” level of FD is unknown. Here, using fish surveys in two representative temperate and tropical rivers, with a quasi-exhaustive genetic and trait database, we measured the bias and variability of different FD indices when calculated with uncertainty in taxonomic assignment at the genus and family level. Our results show that when measuring FD indices with species randomly chosen within genera and families, the bias cannot exceed 30% from real observed FD values. The variability is higher for species-poorer communities and when those communities are composed of genera and families with high functional heterogeneity. Despite taxonomic uncertainty, our results demonstrate the potential of eDNA surveys to estimate reliable FD values.

Published
2023
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36. Long‐duration remote underwater videos reveal that grazing by fishes is highly variable through time and dominated by non‐indigenous species

Author

Magneville, Camille, Leréec Le Bricquir, Marie‐lou, Dailianis, Thanos, Skouradakis, Grigorios, Claverie, Thomas, Villéger, Sébastien, Magneville, Camille, Leréec Le Bricquir, Marie‐lou, Dailianis, Thanos, Skouradakis, Grigorios, Claverie, Thomas, and Villéger, Sébastien

Abstract

In the marine environment, fish contribute to key ecological processes such as controlling food-webs through top-down impacts, especially on algae. To date, the assessment of fish grazing activity has mostly been performed using short-term (<1 h) censuses by divers or remote cameras which do not allow estimating the variability of grazing rate within and between days. However, understanding the temporal variation of fish activity and hence contribution of species to ecosystem functioning is of particular interest in the context of biological invasion. Here, using long-duration remote underwater cameras, we recorded fish abundance and grazing events over three consecutive days in October 2019 in a shallow Mediterranean ecosystem from northern Crete. This novel approach allowed us to assess temporal variation of abundance and grazing activity of the two native (Sarpa salpa and Sparisoma cretense) and the two non-indigenous fish species (Siganus rivulatus and Siganus luridus). Non-indigenous Siganus rivulatus was the most common species in the studied coastal habitat, followed by the two native species while the non-indigenous Siganus luridus was scarce. Overall, the non-indigenous S. rivulatus and the native S. salpa are responsible for more than 90% of the recorded grazing activity with similar bite rates between the two species. More than 70% of the grazing activity arose in grazing pulses in the afternoon, supporting the diel feeding hypothesis according to which feeding is greater in the afternoon when nutritive quality of macrophytes is the highest. In addition, some of the highest peaks in grazing activity were driven by a few individuals. Hence, surveys of only abundance could not provide accurate estimates of herbivory. Last, Siganus rivulatus presence did not significantly affect grazing activity of the native Sarpa salpa. Our results demonstrate that long-duration remote underwater videos are a useful tool to accurately assess the contribution of fishes to e

Published
2023
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38. The role of fish feces for nutrient cycling on coral reefs.

Author

Schiettekatte, Nina M. D., Casey, Jordan M., Brandl, Simon J., Mercière, Alexandre, Degregori, Sam, Burkepile, Deron, Van Wert, Jacey C., Ghilardi, Mattia, Villéger, Sébastien, and Parravicini, Valeriano

Subjects
CORAL reefs & islands, NUTRIENT cycles, CORALS, CORAL reef fishes, BIOGEOCHEMICAL cycles
Abstract

Consumers play an important role in biogeochemical cycles through the consumption and release of essential elements such as carbon (C), nitrogen (N), and phosphorus (P). Indeed, a large proportion of consumed elements are released into the environment in inorganic (i.e. excretion) or organic form (i.e. egestion). On coral reefs, fishes represent the bulk of consumer biomass and thus play a key role in the recycling of nutrients. In recent years, excretion rates have been studied intensively, but less is known about the rate and quality of coral reef fish egestion. In this study, we quantify the elemental contents of fish feces, estimate absorption efficiencies and compare egestion and excretion rates for 51 coral reef fish species. We show that elemental concentrations decrease remarkably little from food to feces. This is due to extremely low absorption efficiencies, resulting in the egestion of large amounts of energy and nutrients. Moreover, we show that while the quality of fish feces varies across trophic guilds, it remains highly variable within trophic guilds. Finally, we demonstrate that the release of N and P through egestion outweighs the amount of nutrients recycled through excretion. Our study highlights the need to incorporate animal egestion into assessments of ecosystem functioning and food web structure. [ABSTRACT FROM AUTHOR]

Published
2023
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46. An invasive herbivorous fish (Siganus rivulatus) influences both benthic and planktonic microbes through defecation and nutrient excretion

Author

Escalas, Arthur, primary, Avouac, Amandine, additional, Belmaker, Jonathan, additional, Bouvier, Thierry, additional, Clédassou, Valentin, additional, Ferraton, Franck, additional, Rieuvilleneuve, Fabien, additional, Rilov, Gil, additional, Rovirosa Mulet, Anna, additional, Shapiro Goldberg, Daphna, additional, and Villéger, Sébastien, additional

Published
2022
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