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2. Anticipating the effects of climate warming and natural habitat conversion on waterbird communities to address protection gaps

Author

Verniest, Fabien, Le Viol, Isabelle, Julliard, Romain, Dami, Laura, Guelmami, Anis, Suet, Marie, Abdou, Wed, Azafzaf, Hichem, Bendjedda, Nadjiba, Bino, Taulant, Borg, John J., Božič, Luka, Dakki, Mohamed, El Hamoumi, Rhimou, Encarnação, Vitor, Erciyas-Yavuz, Kiraz, Etayeb, Khaled, Georgiev, Valeri, Hamada, Ayman, Hatzofe, Ohad, Ieronymidou, Christina, Langendoen, Tom, Mikuska, Tibor, Molina, Blas, Moniz, Filipe, Moussy, Caroline, Ouassou, Asmaâ, Petkov, Nicky, Portolou, Danae, Qaneer, Tareq, Sayoud, Samir, Šćiban, Marko, Topić, Goran, Uzunova, Danka, Vine, Gal, Vizi, Andrej, Xeka, Erald, Zenatello, Marco, Gaget, Elie, and Galewski, Thomas

Published
2023
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3. Estimation of species relative abundances and habitat preferences using opportunistic data

Author

Coron, Camille, Calenge, Clément, Giraud, Christophe, and Julliard, Romain

Subjects
Statistics - Applications
Abstract

We develop a new statistical procedure to monitor, with opportunist data, relative species abundances and their respective preferences for dierent habitat types. Following Giraud et al. (2015), we combine the opportunistic data with some standardized data in order to correct the bias inherent to the opportunistic data collection. Our main contributions are (i) to tackle the bias induced by habitat selection behaviors, (ii) to handle data where the habitat type associated to each observation is unknown, (iii) to estimate probabilities of selection of habitat for the species. As an illustration, we estimate common bird species habitat preferences and abundances in the region of Aquitaine (France).

Published
2017

4. Exposure of wetlands important for nonbreeding waterbirds to sea‐level rise in the Mediterranean.

Author

Verniest, Fabien, Galewski, Thomas, Boutron, Olivier, Dami, Laura, Defos du Rau, Pierre, Guelmami, Anis, Julliard, Romain, Popoff, Nadège, Suet, Marie, Willm, Loïc, Abdou, Wed, Azafzaf, Hichem, Bendjedda, Nadjiba, Bino, Taulant, Borg, John J., Božič, Luka, Dakki, Mohamed, Hamoumi, Rhimou El, Encarnação, Vitor, and Erciyas‐Yavuz, Kiraz

Abstract

Copyright of Conservation Biology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2024
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5. Guidance framework to apply good practices in ecological data analysis: Lessons learned from building Galaxy-Ecology

Author

ROYAUX, Coline, primary, Mihoub, Jean-Baptiste, additional, Jossé, Marie, additional, Pelletier, Dominique, additional, Norvez, Olivier, additional, Reecht, Yves, additional, Fouilloux, Anne, additional, Rasche, Helena, additional, Hiltemann, Saskia, additional, Batut, Bérénice, additional, Eléaume, Marc, additional, Seguineau, Pauline, additional, Massé, Guillaume, additional, Amossé, Alan, additional, Bissery, Claire, additional, Lorrilliere, Romain, additional, Martin, Alexis, additional, Bas, Yves, additional, Virgoulay, Thimothée, additional, Chambon, Valentin, additional, Arnaud, Elie, additional, Michon, Elisa, additional, Urfer, Clara, additional, Trigodet, Eloïse, additional, Delannoy, Marie, additional, Loïs, Gregoire, additional, Julliard, Romain, additional, Grüning, Björn, additional, and Le Bras, Yvan, additional

Published
2024
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7. Guidance framework to apply good practices in ecological data analysis: Lessons learned from building Galaxy-Ecology

Author

Royaux, Coline, Mihoub, Jean-baptiste, Jossé, Marie, Pelletier, Dominique, Norvez, Olivier, Reecht, Yves, Fouilloux, Anne, Rasche, Helena, Hiltemann, Saskia, Batut, Bérénice, Eléaume, Marc, Seguineau, Pauline, Massé, Guillaume, Amossé, Alan, Bissery, Claire, Lorrilliere, Romain, Martin, Alexis, Bas, Yves, Virgoulay, Thimothée, Chambon, Valentin, Arnaud, Elie, Michon, Elisa, Urfer, Clara, Trigodet, Eloïse, Delannoy, Marie, Loïs, Gregoire, Julliard, Romain, Grüning, Björn, Le Bras, Yvan, The 17 Galaxy-e Community, Royaux, Coline, Mihoub, Jean-baptiste, Jossé, Marie, Pelletier, Dominique, Norvez, Olivier, Reecht, Yves, Fouilloux, Anne, Rasche, Helena, Hiltemann, Saskia, Batut, Bérénice, Eléaume, Marc, Seguineau, Pauline, Massé, Guillaume, Amossé, Alan, Bissery, Claire, Lorrilliere, Romain, Martin, Alexis, Bas, Yves, Virgoulay, Thimothée, Chambon, Valentin, Arnaud, Elie, Michon, Elisa, Urfer, Clara, Trigodet, Eloïse, Delannoy, Marie, Loïs, Gregoire, Julliard, Romain, Grüning, Björn, Le Bras, Yvan, and The 17 Galaxy-e Community

Abstract

Numerous conceptual frameworks exist for good practices in research data and analysis (e.g. Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework to achieve good practices for building analytical procedures based on atomisation and generalisation. We introduce the concept of atomisation to identify analytical steps which support generalisation by allowing us to go beyond single analyses. These guidelines were established during the development of the Galaxy-Ecology initiative, a web platform dedicated to data analysis in ecology. Galaxy-Ecology allows us to demonstrate a way to reach higher levels of reproducibility in ecological sciences by increasing the accessibility and reusability of analytical workflows once atomised and generalised.

Published
2024
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9. Capitalising on Opportunistic Data for Monitoring Species Relative Abundances

Author

Giraud, Christophe, Calenge, Clément, Coron, Camille, and Julliard, Romain

Subjects
Statistics - Applications
Abstract

With the internet, a massive amount of information on species abundance can be collected under citizen science programs. However, these data are often difficult to use directly in statistical inference, as their collection is generally opportunistic, and the distribution of the sampling effort is often not known. In this paper, we develop a general statistical framework to combine such "opportunistic data" with data collected using schemes characterized by a known sampling effort. Under some structural assumptions regarding the sampling effort and detectability, our approach allows to estimate the relative abundance of several species in different sites. It can be implemented through a simple generalized linear model. We illustrate the framework with typical bird datasets from the Aquitaine region, south-western France. We show that, under some assumptions, our approach provides estimates that are more precise than the ones obtained from the dataset with a known sampling effort alone. When the opportunistic data are abundant, the gain in precision may be considerable, especially for the rare species. We also show that estimates can be obtained even for species recorded only in the opportunistic scheme. Opportunistic data combined with a relatively small amount of data collected with a known effort may thus provide access to accurate and precise estimates of quantitative changes in relative abundance over space and/or time.

Published
2014

13. Case Studies of Capacity Building for Biodiversity Monitoring

Author

Schmeller, Dirk S., Arvanitidis, Christos, Böhm, Monika, Brummitt, Neil, Chatzinikolaou, Eva, Costello, Mark J., Ding, Hui, Gill, Michael J., Haase, Peter, Julliard, Romain, García-Moreno, Jaime, Pettorelli, Nathalie, Peng, Cui, Riginos, Corinna, Schmiedel, Ute, Simaika, John P., Waterman, Carly, Wu, Jun, Xu, Haigen, Belnap, Jayne, Walters, Michele, editor, and Scholes, Robert J., editor

Published
2017
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18. AlgaeTraits: a trait database for (European) seaweeds

Author

Vranken, Sofie, primary, Robuchon, Marine, additional, Dekeyzer, Stefanie, additional, Bárbara, Ignacio, additional, Bartsch, Inka, additional, Blanfuné, Aurélie, additional, Boudouresque, Charles-François, additional, Decock, Wim, additional, Destombe, Christophe, additional, de Reviers, Bruno, additional, Díaz-Tapia, Pilar, additional, Herbst, Anne, additional, Julliard, Romain, additional, Karez, Rolf, additional, Kersen, Priit, additional, Krueger-Hadfield, Stacy A., additional, Kuhlenkamp, Ralph, additional, Peters, Akira F., additional, Peña, Viviana, additional, Piñeiro-Corbeira, Cristina, additional, Rindi, Fabio, additional, Rousseau, Florence, additional, Rueness, Jan, additional, Schubert, Hendrik, additional, Sjøtun, Kjersti, additional, Sansón, Marta, additional, Smale, Dan, additional, Thibaut, Thierry, additional, Valero, Myriam, additional, Vandepitte, Leen, additional, Vanhoorne, Bart, additional, Vergés, Alba, additional, Verlaque, Marc, additional, Vieira, Christophe, additional, Le Gall, Line, additional, Leliaert, Frederik, additional, and De Clerck, Olivier, additional

Published
2023
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24. Dossier : Des recherches participatives dans la production des savoirs liés à l’environnement – Science participative et suivi de la biodiversité : l’expérience Vigie-Nature★

Author

Julliard Romain

Subjects
écologie, histoire naturelle, muséum, naturalistes, témoignage, Science, Social Sciences
Abstract

Depuis 1989 avec le programme STOC (Suivi temporel des oiseaux communs), mais surtout depuis 2006 et les débuts de Vigie-Nature, un laboratoire du Muséum national d’histoire naturelle contribue avec un ensemble de partenaires à mettre en place un vaste programme de science participative dont l’objectif est d’alimenter des bases de données d’observations standardisées afin de suivre l’état de santé de la biodiversité métropolitaine. Il s’agit ici d’un témoignage de cette aventure par l’un de ses principaux protagonistes, ainsi que d’une modeste tentative de mise en perspective, historique, d’une part, autoréflexive et prospective, d’autre part. Si le succès d’estime est bien là, il reste modéré et fragile par bien des aspects, notamment si l’on mesure le taux de participation et la place des participants dans ces démarches de recherche. L’auteur fait néanmoins le pari que ces sciences participatives ont un potentiel transformatif que le projet « 65 millions d’observateurs » qui débute pourrait permettre de mettre en œuvre.

Published
2017
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26. AlgaeTraits: A trait database for (European) seaweeds

Author

Vranken, Sofie, Robuchon, Marine, Dekeyzer, Stefanie, Bárbara, Ignacio, Bartsch, Inka, Blanfuné, Aurélie, Boudouresque, Charles François, Decock, Wim, Destombe, Christophe, De Reviers, Bruno, Díaz-Tapia, Pilar, Herbst, Anne, Julliard, Romain, Karez, Rolf, Kersen, Priit, Krueger-Hadfield, Stacy A., Kuhlenkamp, Ralph, Peters, Akira F., Peña, Viviana, Piñeiro-Corbeira, Cristina, Rindi, Fabio, Rousseau, Florence, Rueness, Jan, Schubert, Hendrik, Sjøtun, Kjersti, Sansón, Marta, Smale, Dan, Thibaut, Thierry, Valero, Myriam, Vandepitte, Leen, Vanhoorne, Bart, Vergés, Alba, Verlaque, Marc, Vieira, Christophe, Le Gall, Line, Leliaert, Frederik, De Clerck, Olivier, Vranken, Sofie, Robuchon, Marine, Dekeyzer, Stefanie, Bárbara, Ignacio, Bartsch, Inka, Blanfuné, Aurélie, Boudouresque, Charles François, Decock, Wim, Destombe, Christophe, De Reviers, Bruno, Díaz-Tapia, Pilar, Herbst, Anne, Julliard, Romain, Karez, Rolf, Kersen, Priit, Krueger-Hadfield, Stacy A., Kuhlenkamp, Ralph, Peters, Akira F., Peña, Viviana, Piñeiro-Corbeira, Cristina, Rindi, Fabio, Rousseau, Florence, Rueness, Jan, Schubert, Hendrik, Sjøtun, Kjersti, Sansón, Marta, Smale, Dan, Thibaut, Thierry, Valero, Myriam, Vandepitte, Leen, Vanhoorne, Bart, Vergés, Alba, Verlaque, Marc, Vieira, Christophe, Le Gall, Line, Leliaert, Frederik, and De Clerck, Olivier

Abstract

The analysis of biological and ecological traits has a long history in evolutionary and ecological research. However, trait data are often scattered and standardised terminology that transcends taxonomic and biogeographical context are generally missing. As part of the development of a global trait database of marine species, we collated trait information for European seaweeds and structured the data within the standardised framework of the World Register of Marine Species (WoRMS). We collected 45175 trait records for 21 biologically and ecologically relevant traits of seaweeds. This resulted in a trait database for 1745 European seaweed species of which more than half (56%) of the records were documented at the species level, while the remaining 44% were documented at a higher taxonomic level and subsequently inherited at lower levels. The trait database for European seaweeds will serve as a foundation for future research on diversity and evolution of seaweeds and their responses to global changes. The data will contribute to developing detailed trait-based ecosystem models and will be an important tool to inform marine conservation policies. The data are publicly accessible through the AlgaeTraits portal, 10.14284/574 (AlgaeTraits, 2022).

Published
2023

31. Towards a global terrestrial species monitoring program

Author

Schmeller, Dirk S., Julliard, Romain, Bellingham, Peter J., Böhm, Monika, Brummitt, Neil, Chiarucci, Alessandro, Couvet, Denis, Elmendorf, Sarah, Forsyth, David M., Moreno, Jaime García, Gregory, Richard D., Magnusson, William E., Martin, Laura J., McGeoch, Melodie A., Mihoub, Jean-Baptiste, Pereira, Henrique M., Proença, Vânia, van Swaay, Chris A.M., Yahara, Tetsukazu, and Belnap, Jayne

Published
2015
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32. Predictive ecology in a changing world

Author

Mouquet, Nicolas, Lagadeuc, Yvan, Devictor, Vincent, Doyen, Luc, Duputié, Anne, Eveillard, Damien, Faure, Denis, Garnier, Eric, Gimenez, Olivier, Huneman, Philippe, Jabot, Franck, Jarne, Philippe, Joly, Dominique, Julliard, Romain, Kéfi, Sonia, Kergoat, Gael J., Lavorel, Sandra, Le Gall, Line, Meslin, Laurence, Morand, Serge, Morin, Xavier, Morlon, Hélène, Pinay, Gilles, Pradel, Roger, Schurr, Frank M., Thuiller, Wilfried, and Loreau, Michel

Published
2015

35. Le lapin de garenne dans les grands parcs paysagers de la Seine-Saint-Denis

Author

Martin, Léo, Chlous, Frédérique, Marmet, Julie, and Julliard, Romain

Subjects
History, histoire longue durée, sciences humaines et sociales, HIS013000, RND, environnement, POL044000, HBJD, biodiversité
Abstract

L’histoire des relations anthropozoologiques du lapin de garenne est longue, singulière et pleine de « rebondissements ». Originaire de la péninsule ibérique, Oryctolagus cuniculus (Linnaeus, 1758) est déplacé par les hommes dès l’Antiquité sur certaines îles de la Méditerranée. À partir du Moyen Âge, le lapin est diffusé par les hommes de manière spectaculaire à travers l’Europe, notamment grâce à la multiplication des garennes. Cette diffusion se poursuivra jusqu’aux temps modernes et conte...

Published
2022

36. Sales bêtes ! Mauvaises herbes !

Author

Arthur, Christian, Astoul Delseny, Julien, Atlan, Anne, Aulagnier, Stéphane, Baron, Nicolas, Beau, Rémi, Béchet, Arnaud, Brugidou, Jérémie, Chansigaud, Valérie, Chlous, Frédérique, Clouette, Fabien, Darrot, Catherine, Desroy, Nicolas, Faget, Daniel, Fourche, Rémi, Fournier, Jérôme, Godet, Laurent, Guinot-Ghestem, Murielle, Guizard, Fabrice, Haffner, Patrick, Jaffeux, Henri, Julliard, Romain, Kohler, Florent, Lathuillière, Laurent, Léna, Philippe, Le Mao, Patrick, Luglia, Rémi, Marchand, Guillaume, Marmet, Julie, Martin, Léo, Mathevet, Raphaël, Micoud, André, Moutou, François, Muxart, Virginie, Olivier, Anthony, Profit, Geneviève, Riguelle, William, Ruette, Sandrine, Thiébaut, Éric, Thierry, Chloé, Treillard, Aline, Udo, Nathalie, and Luglia, Rémi

Subjects
History, histoire longue durée, sciences humaines et sociales, HIS013000, RND, environnement, POL044000, HBJD, biodiversité
Abstract

Depuis plus d’un siècle la notion de « nuisible » fait l’objet d’une contestation de plus en plus vive. Pourtant elle connaît une singulière persistance sociale en tant que concept opérationnel qui donne aux hommes une certaine légitimité pour gérer, et souvent détruire, certaines espèces. À l’heure où la France vient d’adopter la loi sur la reconquête de la biodiversité, la question des « nuisibles » reprend une singulière acuité avec la multiplication d’espèces exotiques envahissantes et les vives controverses qui demeurent autour du loup, du renard mais aussi de l’utilisation des insecticides et des herbicides pour se défaire de « gêneurs ». Si la notion de « nuisible » demeure centrale dans la gestion du sauvage par nos sociétés, elle s’avère très variable selon l’époque, l’espèce, le territoire ou le groupe social considéré. Pour dresser un état de la recherche, historiciser cette notion et éclairer les enjeux actuels, il convient de croiser les regards afin de caractériser les différentes conceptions de la notion de « nuisible » qui coexistent actuellement et d’en retracer les origines, tout en s’ouvrant aux acteurs du présent. Ainsi cet ouvrage entend contribuer à explorer les interactions entre les sociétés et la nature, et permettre de mieux saisir leurs coévolutions.

Published
2022

38. AlgaeTraits: a trait database for (European) seaweeds

Author

Vranken, Sofie, primary, Robuchon, Marine, additional, Dekeyzer, Stefanie, additional, Bárbara, Ignacio, additional, Bartsch, Inka, additional, Blanfuné, Aurélie, additional, Boudouresque, Charles-François, additional, Decock, Wim, additional, Destombe, Christophe, additional, de Reviers, Bruno, additional, Díaz-Tapia, Pilar, additional, Herbst, Anne, additional, Julliard, Romain, additional, Karez, Rolf, additional, Kersen, Priit, additional, Krueger-Hadfield, Stacy A., additional, Kuhlenkamp, Ralph, additional, Peters, Akira F., additional, Peña, Viviana, additional, Piñeiro-Corbeira, Cristina, additional, Rindi, Fabio, additional, Rousseau, Florence, additional, Rueness, Jan, additional, Schubert, Hendrik, additional, Sjøtun, Kjersti, additional, Sansón, Marta, additional, Smale, Dan, additional, Thibaut, Thierry, additional, Valero, Myriam, additional, Vandepitte, Leen, additional, Vanhoorne, Bart, additional, Vergés, Alba, additional, Verlaque, Marc, additional, Vieira, Christophe, additional, Le Gall, Line, additional, Leliaert, Frederik, additional, and De Clerck, Olivier, additional

Published
2022
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46. Citizen science: producing data with people for innovating research

Author

Andrzejewski, Szymon and Julliard, Romain

Subjects
citizen science, open science
Abstract

Most people are able to produce high value data using their observation capacities and following guidelines, and willing to do so provided that it makes sense and that they learn from their participation. Moreover, these data may be enriched by each contributor's local kwoledge, intention, interpretation, leading to unique data that cannot be produced by other means. Data sharing among participants may further improve data quality (e.g., organized quality control) and develop sense of belonging, a strong motivation for participation. Designing citizen science in such way open avenues for innovative research, particularly in the context of the socio-ecological transition we are facing., Co-funded by the Erasmus+ Programme of the European Union

Published
2022
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47. CITIZEN SCIENCE FOR PUBLIC DELIBERATION OF LOCAL ENVIRONMENT POLICIES.

Author

BEDESSEM, BAPTISTE, SOURDRIL, ANNE, BAUMSTARK, VALENTIN, DOS SANTOS, LUCIE, GONZALEZ, EMMANUELLE, PELLETIER, CELINE, STEINMAN, QUENTIN, VERLHAC, LAURA, and JULLIARD, ROMAIN

Subjects
CITIZEN science, POLITICAL participation, DELIBERATION, SCIENTIFIC literature, SCIENTIFIC knowledge, MUNICIPAL lighting, DRAWING
Abstract

Broadening citizen participation in scientific knowledge production has become a priority of national and supra-national institutions and research agencies. Out of their interest for scientific research and public learning, citizen science projects are often presented as offering a unique opportunity to involve more directly the public in policy-making. However, despite twenty years of flourishment of participative scientific research, making citizen science a tool to foster participatory democracy remains a challenge. Political outputs of citizen science are indeed often restricted to its role in the production of data to inform policy making processes. In this paper, we propose an innovative theoretical model of democratization through citizen science, in which participative data collection is associated with public online deliberation. Drawing both on online political deliberation research and citizen science literature, we argue that citizens' engagement in contributory science could help create the conditions of good-quality public deliberations. We then present a technical device (an online platform) that put this model into practice in the context of the regulation of public lighting in two French municipalities. [ABSTRACT FROM AUTHOR]

Published
2023
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48. Case Studies of Capacity Building for Biodiversity Monitoring

Author

Schmeller, Dirk S., primary, Arvanitidis, Christos, additional, Böhm, Monika, additional, Brummitt, Neil, additional, Chatzinikolaou, Eva, additional, Costello, Mark J., additional, Ding, Hui, additional, Gill, Michael J., additional, Haase, Peter, additional, Julliard, Romain, additional, García-Moreno, Jaime, additional, Pettorelli, Nathalie, additional, Peng, Cui, additional, Riginos, Corinna, additional, Schmiedel, Ute, additional, Simaika, John P., additional, Waterman, Carly, additional, Wu, Jun, additional, Xu, Haigen, additional, and Belnap, Jayne, additional

Published
2016
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