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| Registros recuperados: 66 | |
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| 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 H. M.; Meyer, Christoph F. J.; 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; Chase, Jonathan M.. |
| 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... |
| Tipo: Text |
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| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00604/71606/70047.pdf |
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| Villon, Sébastien; Mouillot, David; Chaumont, Marc; Subsol, Gérard; Claverie, Thomas; Villéger, Sébastien. |
| Processing data from surveys using photos or videos remains a major bottleneck in ecology. Deep Learning Algorithms (DLAs) have been increasingly used to automatically identify organisms on images. However, despite recent advances, it remains difficult to control the error rate of such methods. Here, we proposed a new framework to control the error rate of DLAs. More precisely, for each species, a confidence threshold was automatically computed using a training dataset independent from the one used to train the DLAs. These species-specific thresholds were then used to post-process the outputs of the DLAs, assigning classification scores to each class for a given image including a new class called “unsure”. We applied this framework to a study case... |
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| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00640/75244/75406.pdf |
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| Kadarusman,; Sugeha, Hagi Yulia; Pouyaud, Laurent; Hocdé, Régis; Hismayasari, Intanurfemi B.; Gunaisah, Endang; Widiarto, Santoso B.; Arafat, Gulam; Widyasari, Ferliana; Mouillot, David; Paradis, Emmanuel. |
| Coelacanth fishes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled about the diversity and evolutionary history of these ‘living fossils’ using new molecular data, including the possibility of ‘cryptic’ species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750 km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living... |
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| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00603/71466/69921.pdf |
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| Escalas, Arthur; Bouvier, Thierry; Mouchet, Maud A.; Leprieur, Fabien; Bouvier, Corinne; Troussellier, Marc; Mouillot, David. |
| Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (), regional () and the overall difference between local communities (). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically... |
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| Ano: 2013 |
URL: http://archimer.ifremer.fr/doc/00163/27441/25668.pdf |
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| Mouillot, David; Gaillard, Sylvain; Aliaume, Catherine; Verlaque, Marc; Belsher, Thomas; Troussellier, Marc; Chi, Thang. |
| Lagoons are highly productive areas representing more than 50% of the coastline area in Languedoc-Roussillon (South of France, Mediterranean sea). These lagoons are very different in their environmental conditions, human influences, eutrophication levels and aquaculture intensity. Based on macrophyte communities associated with soft substrates, two indices of taxonomic diversity (the "average taxonomic distinctness" (Delta(+)) and the "variation in taxonomic distinctness" (Lambda(+))) were used to discriminate four of these lagoons (Thau, Salse-Leucate, Bages-Sigean and Mauguio). Bages-Sigean presented a significant higher average taxonomic distinctness (p < 0.05) and Salse-Leucate had a significant higher variation in taxonomic distinctness (p <... |
| Tipo: Text |
Palavras-chave: Languedoc Roussillon; Exotic species; Human impact; Eutrophication; Biodiversity. |
| Ano: 2005 |
URL: http://archimer.ifremer.fr/doc/2005/publication-748.pdf |
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| Juhel, Jean-baptiste; Utama, Rizkie S.; Marques, Virginie; Vimono, Indra B.; Sugeha, Hagi Yulia; Kadarusman,; Pouyaud, Laurent; Dejean, Tony; Mouillot, David; Hocdé, Régis. |
| Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species... |
| Tipo: Text |
Palavras-chave: EDNA metabarcoding; Sequence clustering; Operational Taxonomic Unit; Diversity assessment; Detectability. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00640/75232/79601.pdf |
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| Andrello, Marco; Mouillot, David; Somot, Samuel; Thuiller, Wilfried; Manel, Stephanie. |
| AimTo study the combined effects of climate change on connectivity between marine protected areas (MPAs) and larval supply to the continental shelf. LocationThe Mediterranean Sea, where sea surface temperatures are expected to strongly increase by the end of the 21st century, represents an archetypal situation with a dense MPA network but resource overexploitation outside. MethodsUsing an individual-based mechanistic model of larval transport, forced with an emission-driven regional climate change scenario for the Mediterranean Sea, we explored the combined effects of changes in hydrodynamics, adult reproductive timing and larval dispersal on the connectivity among MPAs and their ability to seed fished areas with larvae. ResultsWe show that, over the... |
| Tipo: Text |
Palavras-chave: Biophysical model; Conservation planning; Epinephelus marginatus; Larval dispersal; Larval growth rate; Reproductive timing. |
| Ano: 2015 |
URL: https://archimer.ifremer.fr/doc/00627/73867/73398.pdf |
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| Magris, Rafael A.; Andrello, Marco; Pressey, Robert L.; Mouillot, David; Dalongeville, Alicia; Jacobi, Martin N.; Manel, Stephanie. |
| Current methods in conservation planning for promoting the persistence of biodiversity typically focus on either representing species geographic distributions or maintaining connectivity between reserves, but rarely both, and take a focal species, rather than a multispecies, approach. Here, we link prioritization methods with population models to explore the impact of integrating both representation and connectivity into conservation planning for species persistence. Using data on 288 Mediterranean fish species with varying conservation requirements, we show that: (1) considering both representation and connectivity objectives provides the best strategy for enhanced biodiversity persistence and (2) connectivity objectives were fundamental to enhancing... |
| Tipo: Text |
Palavras-chave: Biodiversity conservation; Larval dispersal; Marine protected areas; Marine reserve design; Spatial planning; Spatial prioritization. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00454/56593/74958.pdf |
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| Marques, Virginie; Guérin, Pierre-édouard; Rocle, Mathieu; Valentini, Alice; Manel, Stéphanie; Mouillot, David; Dejean, Tony. |
| Human activities impact all ecosystems on Earth, which urges scientists to better understand biodiversity changes across temporal and spatial scales. Environmental DNA (eDNA) metabarcoding is a promising non‐invasive method to assess species composition in a wide range of ecosystems. Yet, this method requires the completeness of a reference database, i.e. a list of DNA sequences attached to each species of the regional pool, which is rarely met. As an alternative, molecular operational taxonomic units (MOTUs) can be extracted as clusters of sequences. However, the extent to which the diversity of MOTUs can predict the diversity of species across spatial scales is unknown. Here, we used 196 samples along the Rhone river (France) for which the reference... |
| Tipo: Text |
Palavras-chave: 12S primer; Alpha-beta-delta-diversity; Clustering; Metabarcoding; MOTUs; Reference database. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00643/75506/76373.pdf |
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| Cinner, Joshua E.; Huchery, Cindy; Macneil, M. Aaron; Graham, Nicholas A. J.; Mcclanahan, Tim R.; Maina, Joseph; Maire, Eva; Kittinger, John N.; Hicks, Christina C.; Mora, Camilo; Allison, Edward H.; D'Agata, Stephanie; Hoey, Andrew; Feary, David A.; Crowder, Larry; Williams, Ivor D.; Kulbicki, Michel; Vigliola, Laurent; Wantiez, Laurent; Edgar, Graham; Stuart-smith, Rick D.; Sandin, Stuart A.; Green, Alison L.; Hardt, Marah J.; Beger, Maria; Friedlander, Alan; Campbell, Stuart J.; Holmes, Katherine E.; Wilson, Shaun K.; Brokovich, Eran; Brooks, Andrew J.; Cruz-motta, Juan J.; Booth, David J.; Chabanet, Pascale; Gough, Charlie; Tupper, Mark; Ferse, Sebastian C. A.; Sumaila, U. Rashid; Mouillot, David. |
| Ongoing declines in the structure and function of the world's coral reefs(1,2) require novel approaches to sustain these ecosystems and the millions of people who depend on them(3). A presently unexplored approach that draws on theory and practice in human health and rural development(4,5) is to systematically identify and learn from the 'outliers'-places where ecosystems are substantially better ('bright spots') or worse ('dark spots') than expected, given the environmental conditions and socioeconomic drivers they are exposed to. Here we compile data from more than 2,500 reefs worldwide and develop a Bayesian hierarchical model to generate expectations of how standing stocks of reef fish biomass are related to 18 socioeconomic drivers and environmental... |
| Tipo: Text |
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| Ano: 2016 |
URL: https://archimer.ifremer.fr/doc/00348/45872/68023.pdf |
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| Rocklin, Delphine; Santoni, Marie-catherine; Culioli, Jean-michel; Tomasini, Jean-antoine; Pelletier, Dominique; Mouillot, David. |
| There is increasing evidence from previous studies, and from fishers' observations, that coastal dolphins use fishing nets as an easily accessible feeding source, damaging or depredating fish caught in the nets. This study investigates the impact of dolphin depredation on artisanal trammelnets by analysing the catch composition of 614 artisanal fishing operations in the Bonifacio Strait Natural Reserve (France). Common bottlenose dolphins (Tursiops truncatus) attacked, on average, 12.4% of the nets and damaged 8.3% of the catch. However, attacked nets were characterized by statistically significantly higher catch per unit effort than unattacked ones. Catch composition also differed significantly after dolphin attacks; bentho-pelagic fish were more... |
| Tipo: Text |
Palavras-chave: Marine protected area; Interactions with fisheries; Depredation; Catch per unit effort; Catch composition; Bottlenose dolphin; Artisanal fisheries. |
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6808.pdf |
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| Maire, Eva; Villeger, Sebastien; Graham, Nicholas A. J.; Hoey, Andrew S.; Cinner, Joshua; Ferse, Sebastian C. A.; Aliaume, Catherine; Booth, David J.; Feary, David A.; Kulbicki, Michel; Sandin, Stuart A.; Vigliola, Laurent; Mouillot, David. |
| Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute, beyond the socio-environmental and species richness effects, to the biomass and coral cover on Indo-Pacific reefs. We found that only a limited set of species (51 out of approx. 400, = approx. 13%), belonging to various... |
| Tipo: Text |
Palavras-chave: Ecosystem functioning; Biodiversity; Fish community; Key species; Ecosystem services; Coral reefs. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00452/56388/68019.pdf |
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| Polanco Fernández, Andrea; Marques, Virginie; Fopp, Fabian; Juhel, Jean‐baptiste; Borrero‐pérez, Giomar Helena; Cheutin, Marie‐charlotte; Dejean, Tony; González Corredor, Juan David; Acosta‐chaparro, Andrés; Hocdé, Régis; Eme, David; Maire, Eva; Spescha, Manuel; Valentini, Alice; Manel, Stéphanie; Mouillot, David; Albouy, Camille; Pellissier, Loïc. |
| Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems such as coral reefs is a prerequisite for their application in long‐term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to... |
| Tipo: Text |
Palavras-chave: Biodiversity; Biomonitoring; Caribbean Sea; Environmental DNA; Reef fishes; Underwater visual census. |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00653/76543/77643.pdf |
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| Juhel, Jean‐baptiste; Marques, Virginie; Polanco Fernández, Andrea; Borrero‐pérez, Giomar H.; Mutis Martinezguerra, Maria; Valentini, Alice; Dejean, Tony; Manel, Stéphanie; Loiseau, Nicolas; Velez, Laure; Hocdé, Régis; Letessier, Tom B.; Richards, Eilísh; Hadjadj, Florine; Bessudo, Sandra; Ladino, Felipe; Albouy, Camille; Mouillot, David; Pellissier, Loïc. |
| Monitoring large marine mammals is challenging due to their low abundances in general, an ability to move over large distances and wide geographical range sizes. The distribution of the pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales is informed by relatively rare sightings, which does not permit accurate estimates of their distribution ranges. Hence, their conservation status has long remained Data Deficient (DD) in the Red list of the International Union for Conservation of Nature (IUCN), which prevent appropriate conservation measures. Environmental DNA (eDNA) metabarcoding uses DNA traces left by organisms in their environments to detect the presence of targeted taxon, and is here proved to be useful to increase our knowledge on the... |
| Tipo: Text |
Palavras-chave: EDNA; Megafauna; Mobile species; Pelagic. |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00683/79484/82076.pdf |
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| Maire, Eva; D'Agata, Stephanie; Aliaume, Catherine; Mouillot, David; Darling, Emily S.; Ramahery, Volanirina; Ranaivoson, Ravaka; Randriamanantsoa, Bemahafaly; Tianarisoa, Tantely F.; Santisy, Abdoul; Cinner, Joshua E.. |
| Rapid degradation of the world’s coral reefs jeopardizes their ecological functioning and ultimately imperils the wellbeing of the millions of people with reef-dependent livelihoods. Ecosystem accessibility is the main driver of their conditions, with the most accessible ecosystems being most at risk of resource depletion. People’s socioeconomic conditions can change as they get further from urban centers and can profoundly influence people’s relationship with the environment. However, the mechanisms through which increasing accessibility from human societies affects natural resources are still unclear. A plausible mechanism through which markets influence the environment is through the socioeconomic changes that tend to accompany accessibility. We used... |
| Tipo: Text |
Palavras-chave: Accessibility; Coral reef fisheries; Fish biomass; Market access; Social-ecological systems. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00652/76440/77528.pdf |
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| Leitao, Rafael P.; Zuanon, Jansen; Mouillot, David; Leal, Cecilia G.; Hughes, Robert M.; Kaufmann, Philip R.; Villeger, Sebastien; Pompeu, Paulo S.; Kasper, Daniele; De Paula, Felipe R.; Ferraz, Silvio F. B.; Gardner, Toby A.. |
| Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the Amazon to date, examining functional responses of fish assemblages to land use. We sampled fish assemblages from two large human-modified regions, and characterized stream conditions by physical habitat attributes and key landscape-change... |
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| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00420/53101/75002.pdf |
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| 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. |
| 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... |
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| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00442/55321/56837.pdf |
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| Registros recuperados: 66 | |
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