%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Ariza, A.
%A Lengaigne, Matthieu
%A Menkès, Christophe
%A Lebourges Dhaussy, Anne
%A Receveur, A.
%A Gorgues, Thomas
%A Habasque, Jérémie
%A Gutierrez, M.
%A Maury, Olivier
%A Bertrand, Arnaud
%T Global decline of pelagic fauna in a warmer ocean
%D 2022
%L fdi:010086398
%G ENG
%J Nature Climate Change
%@ 1758-678X
%K MONDE
%M ISI:000863215100001
%P [22 ]
%R 10.1038/s41558-022-01479-2
%U https://www.documentation.ird.fr/hor/fdi:010086398
%> https://www.documentation.ird.fr/intranet/publi/2022-12/010086398.pdf
%V [Early access]
%W Horizon (IRD)
%X Pelagic fauna is expected to be impacted under climate change according to ecosystem simulations. However, the direction and magnitude of the impact is still uncertain and still not corroborated by observation-based statistical studies. Here we compile a global underwater sonar database and 20 ocean climate projections to predict the future distribution of sound-scattering fauna around the world's oceans. We show that global pelagic fauna will be seriously compromised by the end of the twenty-first century if we continue under the current greenhouse emission scenario. Low and mid latitudes are expected to lose from 3% to 22% of animal biomass due to the expansion of low-productive systems, while higher latitudes would be populated by present-day temperate fauna, supporting results from ecosystem simulations. We further show that strong mitigation measures to contain global warming below 2 degrees C would reduce these impacts to less than half.
%$ 021 ; 032 ; 036

%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Ariza, A.
%A Lengaigne, Matthieu
%A Menkès, Christophe
%A Lebourges Dhaussy, Anne
%A Receveur, A.
%A Gorgues, Thomas
%A Habasque, Jérémie
%A Gutierrez, M.
%A Maury, Olivier
%A Bertrand, Arnaud
%T Global decline of pelagic fauna in a warmer ocean
%D 2022
%L fdi:010086341
%G ENG
%J Nature Climate Change
%@ 1758-678X
%K MONDE
%M ISI:000863854500018
%N 10
%P 928-934 + 15
%R 10.1038/s41558-022-01479-2
%U https://www.documentation.ird.fr/hor/fdi:010086341
%> https://www.documentation.ird.fr/intranet/publi/2022-11/010086341.pdf
%V 12
%W Horizon (IRD)
%X Pelagic fauna is expected to be impacted under climate change according to ecosystem simulations. However, the direction and magnitude of the impact is still uncertain and still not corroborated by observation-based statistical studies. Here we compile a global underwater sonar database and 20 ocean climate projections to predict the future distribution of sound-scattering fauna around the world's oceans. We show that global pelagic fauna will be seriously compromised by the end of the twenty-first century if we continue under the current greenhouse emission scenario. Low and mid latitudes are expected to lose from 3% to 22% of animal biomass due to the expansion of low-productive systems, while higher latitudes would be populated by present-day temperate fauna, supporting results from ecosystem simulations. We further show that strong mitigation measures to contain global warming below 2 degrees C would reduce these impacts to less than half.
%$ 021 ; 034 ; 036 ; 020

%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Salvetat, Julie
%A Bez, Nicolas
%A Habasque, Jérémie
%A Lebourges Dhaussy, Anne
%A Lopes, C.
%A Roudaut, Gildas
%A Simier, Monique
%A Travassos, P.
%A Vargas, G.
%A Bertrand, Arnaud
%T Comprehensive spatial distribution of tropical fish assemblages from multifrequency acoustics and video fulfils the island mass effect framework
%D 2022
%L fdi:010085184
%G ENG
%J Scientific Reports - Nature
%@ 2045-2322
%K ATLANTIQUE ; BRESIL ; ZONE TROPICALE
%K FERNANDO DE NORONHA ARCHIPEL
%M ISI:000799975800085
%N 1
%P 8787 [24 ]
%R 10.1038/s41598-022-12409-9
%U https://www.documentation.ird.fr/hor/fdi:010085184
%> https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2022-07/010085184.pdf
%V 12
%W Horizon (IRD)
%X Tropical marine ecosystems are highly biodiverse and provide resources for small-scale fisheries and tourism. However, precise information on fish spatial distribution is lacking, which limits our ability to reconcile exploitation and conservation. We combined acoustics to video observations to provide a comprehensive description of fish distribution in a typical tropical environment, the Fernando de Noronha Archipelago (FNA) off Northeast Brazil. We identified and classified all acoustic echoes into ten fish assemblage and two triggerfish species. This opened up the possibility to relate the different spatial patterns to a series of environmental factors and the level of protection. We provide the first biomass estimation of the black triggerfish Melichthys niger, a key tropical player. By comparing the effects of euphotic and mesophotic reefs we show that more than the depth, the most important feature is the topography with the shelf-break as the most important hotspot. We also complete the portrait of the island mass effect revealing a clear spatial dissymmetry regarding fish distribution. Indeed, while primary productivity is higher downstream, fish concentrate upstream. The comprehensive fish distribution provided by our approach is directly usable to implement scientific-grounded Marine Spatial Planning.
%$ 034 ; 036

%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Cotté, C.
%A Ariza, A.
%A Berne, A.
%A Habasque, Jérémie
%A Lebourges Dhaussy, Anne
%A Roudaut, Gildas
%A Espinasse, B.
%A Hunt, B. P. V.
%A Pakhomov, E. A.
%A Henschke, N.
%A Péron, C.
%A Conchon, A.
%A Koedooder, C.
%A Izard, L.
%A Cherel, Y.
%T Macrozooplankton and micronekton diversity and associated carbon vertical patterns and fluxes under distinct productive conditions around the Kerguelen Islands
%D 2022
%L fdi:010083336
%G ENG
%J Journal of Marine Systems
%@ 0924-7963
%K Macrozooplankton ; Micronekton ; Vertical patterns ; Active carbon flux ; Spatio-temporal variability ; Scattering layers ; Kerguelen Plateau ; Southern Ocean
%K KERGUELEN ; OCEAN AUSTRALE
%M ISI:000714510000003
%P 103650 [18 ]
%R 10.1016/j.jmarsys.2021.103650
%U https://www.documentation.ird.fr/hor/fdi:010083336
%> https://www.documentation.ird.fr/intranet/publi/2021-12/010083336.pdf
%V 226
%W Horizon (IRD)
%X Mesopelagic communities are characterized by a large biomass of diverse macrozooplankton and micronekton (MM) performing diel vertical migration (DVM) connecting the surface to the deeper ocean and contributing to biogeochemical fluxes. In the Southern Ocean, a prominent High Nutrient Low Chlorophyll (HNLC) and low carbon export region, the contribution of MM to the vertical carbon flux of the biological pump remains largely unknown. Furthermore, few studies have investigated MM communities and vertical flux in naturally iron fertilized areas associated with shallow bathymetry. In this study, we assessed the MM community diversity, abundance and biomass in the Kerguelen Island region, including two stations in the HNLC region upstream of the islands, and two stations in naturally iron fertilized areas, one on the Plateau, and one downstream of the Plateau. The MM community was examined using a combination of trawl sampling and acoustic measurements at 18 and 38 kHz from the surface to 800 m. A conspicuous three-layer vertical system was observed in all areas - a shallow scattering layer, SSL, between 10 and 200 m; mid-depth scattering layer, MSL, between 200 and 500 m; deep scattering layer, DSL, between 500 and 800 m - but communities differing among stations. While salps (Salpa thompsoni) dominated the biomass at the productive Kerguelen Plateau and the downstream station, they were scarce in the HNLC upstream area. In addition, crustaceans (mainly Euphausia vallentini and Themisto gaudichaudii) were particularly abundant over the Plateau, representing a large, although varying, carbon stock in the 0-500 m water layer. Mesopelagic fish were prominent below 400 m where they formed permanent or migrant layers accounting for the main source of carbon biomass. Through these spatial and temporal sources of variability, complex patterns of the MM vertical distribution and associated carbon content were identified. The total carbon flux mediated by migratory myctophids at the four stations was quantified. While this flux was likely underestimated, this study identified the main components and mechanisms of active carbon export in the region and how they are modulated by complex topography and land mass effects.
%$ 034

%0 Unpublished Work
%9 AP : Autres productions
%A Habasque, Jérémie
%A Roudaut, Gildas
%A Perrot, Yannick
%A Lebourges-Dhaussy, Anne
%A Brehmer, Patrice
%T Matecho user manual : version 05
%C Plouzané
%D 2020
%L fdi:010077719
%G ENG
%I LEMAR ; IRD
%P 99  multigr.
%U https://www.documentation.ird.fr/hor/fdi:010077719
%W Horizon (IRD)
%X Matecho is an integrated and supervised Matlab processing chain, which allows realizing scientific echo-sounder data treatments. It allows applying, under user control, recent echo-sounder data processing methods needed to prepare and present acoustic data to their analysis and interpretation in the field of fisheries acoustics researches.
%$ 122

%0 Conference Proceedings
%9 ACTI : Communications avec actes dans un congrès international
%A Perrot, Yannick
%A Brehmer, Patrice
%A Habasque, Jérémie
%A Roudaut, Gildas
%A Behagle, Nolwenn
%A Sarré, A.
%A Diogoul, N.
%A Lebourges Dhaussy, Anne
%T Matecho : an open-source tool for processing fisheries acoustics data to facilitate collaborative development [résumé de poster]
%S International conference ICAWA 2017 and 2018 : extended book of abstract : the AWA project : ecosystem approach to the management of fisheries and the marine environment in West African waters
%C [s.l.]
%D 2019
%E Brehmer, Patrice
%E Diogoul, N.
%E Zenk, C.
%E Vareilles, M. de
%E Keenlyside, N.
%E Nascimento, J.M.
%E Ramos, V. M.
%E Sow, B.A.
%E Fock, H.
%E Schmidt, J.
%E Ekau, W.
%E Mbaye, A.
%E Fall. A.
%E Monteiro, I.
%E Kouassi, A.M.
%E Silva, O.
%E Brochier, Timothée
%E Sall. M.
%E Mayif, M.
%E Koné, V.
%E Gorgues, Thomas
%E Ferreira Santos, C.
%E Bamy, I.L.
%E Barry, I.
%E Sidibe, M.
%E Diadhou, H.
%L fdi:010078279
%G ENG
%I SRFC/CSRP ; IRD
%@ 978-9553602-0-06
%K AFRIQUE DE L'OUEST ; ATLANTIQUE
%P 150
%U https://www.documentation.ird.fr/hor/fdi:010078279
%> https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers20-05/010078279.pdf
%W Horizon (IRD)
%X Matecho is an automated processing method to extract information and perform echo-integration and fish shoal extraction from various scientific echo-sounder sources providing digital acoustic data on fisheries and aquatic ecosystem. The open-source initiative helps foster collaboration and technological transfer. Matecho supports various formats, such as the international standard format for the exchange of fisheries acoustics raw and edited data. The procedure allows the semiautomatic cleaning of echogram data and the application of automatic data filters, i.e., transient noise, attenuated signal and impulsive noise removal and background noise reduction. Echo-integration processing is executed for each depth layer and integrates their characteristics per elementary sampling unit. Sound scattered layers are automatically detected by segmentation from the echo-integrated echogram, and shoals are extracted according to an iterative process of aggregation of filtered echogram echoes that allows, in both cases, the calculation of the ad hoc parameters describing morphological, spatial location and acoustic characteristics of sound scattered layers and shoals. Matecho is open-source software for researchers and provides end users with a user-friendly, free executable program.
%B ICAWA : International Conference AWA
%8 2018/04/17-20
%$ 040 ; 122

%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Perrot, Yannick
%A Brehmer, Patrice
%A Habasque, Jérémie
%A Roudaut, Gildas
%A Behagle, Nolwenn
%A Sarre, A.
%A Lebourges Dhaussy, Anne
%T Matecho : an open-source tool for processing fisheries acoustics data
%D 2018
%L fdi:010073782
%G ENG
%J Acoustics Australia
%@ 1839-2571
%K Echo-sounder ; Echo-integration ; Shoal ; Scattered layers ; Multi-frequency ; Underwater acoustics
%M ISI:000442525800006
%N 2
%P 241-248
%R 10.1007/s40857-018-0135-x
%U https://www.documentation.ird.fr/hor/fdi:010073782
%> https://www.documentation.ird.fr/intranet/publi/2018/09/010073782.pdf
%V 46
%W Horizon (IRD)
%X Matecho is an automated processing method to extract information and perform echo-integration and fish shoal extraction from various scientific echo-sounder sources providing digital acoustic data on fisheries and aquatic ecosystem. The open-source initiative helps foster collaboration and technological transfer. Matecho supports various formats, such as the international standard format for the exchange of fisheries acoustics raw and edited data. The procedure allows the semiautomatic cleaning of echogram data and the application of automatic data filters, i.e., transient noise, attenuated signal and impulsive noise removal and background noise reduction. Echo-integration processing is executed for each depth layer and integrates their characteristics per elementary sampling unit. Sound scattered layers are automatically detected by segmentation from the echo-integrated echogram, and shoals are extracted according to an iterative process of aggregation of filtered echogram echoes that allows, in both cases, the calculation of the ad hoc parameters describing morphological, spatial location and acoustic characteristics of sound scattered layers and shoals. Matecho is open-source software for researchers and provides end users with a user-friendly, free executable program.
%$ 040 ; 122

%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Bertrand, Arnaud
%A Habasque, Jérémie
%A Hattab, T.
%A Hintzen, N. T.
%A Oliveros-Ramos, R.
%A Gutierrez, M.
%A Demarcq, N.
%A Gerlotto, François
%T 3-D habitat suitability of jack mackerel Trachurus murphyi in the Southeastern Pacific, a comprehensive study
%D 2016
%L fdi:010067792
%G ENG
%J Progress in Oceanography
%@ 0079-6611
%K PACIFIQUE SUD ; PEROU ; CHILI
%M ISI:000382341800012
%P 199-211
%R 10.1016/j.pocean.2016.07.002
%U https://www.documentation.ird.fr/hor/fdi:010067792
%> https://www.documentation.ird.fr/intranet/publi/2016/10/010067792.pdf
%V 146
%W Horizon (IRD)
%X South Pacific jack mackerel, Trachurus murphyi, has an ocean-scale distribution, from the South American coastline to New Zealand and Tasmania. This fish, captured by Humans since the Holocene, is nowadays heavily exploited and its population has decreased substantially since the mid-1990s. The uncertainty associated to jack mackerel population structure currently hampers management. Several hypotheses have been proposed from a single population up to several discrete populations. Still no.definitive answer was given. Determining how environmental conditions drive jack mackerel distribution can provide insights on its population structure. To do so, here we performed in three steps. First, we used satellite data to develop a statistical model of jack mackerel horizontal habitat suitability. Model predictions based on interaction between temperature and chlorophyll-a match the observed jack mackerel distribution, even during extreme El Nino event. Second, we studied the impact of oxygen and show that jack mackerel distribution and abundance is correlated to oxygen over a wide variety of scales and avoid low oxygen areas and periods. Third, on the basis of the above we built a conceptual 3D model of jack mackerel habitat in the Southeastern Pacific. We reveal the presence of a low suitable habitat along the Chilean and Peruvian coast, figuratively presenting a closed door caused by a gap in the horizontal habitat at 19-22 S and a shallow oxycline off south-centre Peru. This kind of situation likely occurs on a seasonal basis, in austral summer but also at longer temporal scales. A lack of exchanges at some periods/seasons partially isolate jack mackerel distributed off Peru. On the other hand the continuity in the habitat during most of the year explains why exchanges occur. We conclude that the more likely population structure for jack mackerel is a pelagic metapopulation.
%$ 036 ; 040

%0 Conference Proceedings
%9 ACTI : Communications avec actes dans un congrès international
%A Habasque, Jérémie
%A Bourlès, Bernard
%A Machu, Eric
%A Brehmer, Patrice
%T Multifrequency acoustics measurements during the PIRATA FR25 cruise in the Eastern Tropical Atlantic Ocean
%S International conference ICAWA 2015 : extended book of abstract : the AWA project : ecosystem approach to the management of fisheries and the marine environment in West African waters
%C Dakar
%D 2016
%E Brehmer, Patrice
%E Ba, B.
%E Kraus, G.
%E Gomez, M.M.
%E Diogoul, N.
%E Brandt, P.
%E Sow, B.A.
%E Lazar, A.
%E Capet, X.
%E Fock, H.
%E Machu, Eric
%E Diadihou, H.D.
%E Jouffre, Didier
%E Diallo, I.
%E Schmidt, J.
%E Ekau, W.
%E Gaye, A.
%E Ould Taleb Sidi, M.
%E Thiaw, M.
%E Diop, C.A.
%E Mbaye, A.
%E Gouriou, Yves
%E Traore, D.B.
%E Sall, M.
%E Diara, M.
%E Fall. A.
%E Ly, I.
%E Monteiro, I.
%E Kone, V.
%E Toguyeni, A.
%E Bonnin, Marie
%E Faraj, A.
%L fdi:010067832
%G ENG
%I SRFC/CSRP ; IRD
%@ 978-9553602-0-2
%K AFRIQUE DE L'OUEST ; ATLANTIQUE
%P 73
%U https://www.documentation.ird.fr/hor/fdi:010067832
%> https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers16-07/010067832.pdf
%W Horizon (IRD)
%B International Conference AWA (ICAWA)
%8 2015/11/17-19
%$ 030 ; 040

%0 Conference Proceedings
%9 ACTI : Communications avec actes dans un congrès international
%A Machu, Eric
%A Capet, X.
%A Donval, A.
%A Mbaye, B.C.
%A Habasque, Jérémie
%A Lazar, A.
%A Brehmer, Patrice
%T Observations of plankton communities in the Senegalese upwelling system
%S International conference ICAWA 2015 : extended book of abstract : the AWA project : ecosystem approach to the management of fisheries and the marine environment in West African waters
%C Dakar
%D 2016
%E Brehmer, Patrice
%E Ba, B.
%E Kraus, G.
%E Gomez, M.M.
%E Diogoul, N.
%E Brandt, P.
%E Sow, B.A.
%E Lazar, A.
%E Capet, X.
%E Fock, H.
%E Machu, Eric
%E Diadihou, H.D.
%E Jouffre, Didier
%E Diallo, I.
%E Schmidt, J.
%E Ekau, W.
%E Gaye, A.
%E Ould Taleb Sidi, M.
%E Thiaw, M.
%E Diop, C.A.
%E Mbaye, A.
%E Gouriou, Yves
%E Traore, D.B.
%E Sall, M.
%E Diara, M.
%E Fall. A.
%E Ly, I.
%E Monteiro, I.
%E Kone, V.
%E Toguyeni, A.
%E Bonnin, Marie
%E Faraj, A.
%L fdi:010067826
%G ENG
%I SRFC/CSRP ; IRD
%@ 978-9553602-0-2
%K SENEGAL ; ATLANTIQUE
%P 66
%U https://www.documentation.ird.fr/hor/fdi:010067826
%> https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers16-07/010067826.pdf
%W Horizon (IRD)
%B International Conference AWA (ICAWA)
%8 2015/11/17-19
%$ 034 ; 032

%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Bertrand, Arnaud
%A Grados, D.
%A Habasque, Jérémie
%A Fablet, R.
%A Ballón, M.
%A Castillo, R.
%A Gutiérrez, M.
%A Chaigneau, Alexis
%A Josse, Erwan
%A Roudaut, Gildas
%A Lebourges Dhaussy, Anne
%A Brehmer, Patrice
%T Routine acoustic data as new tools for a 3D vision of the abiotic and biotic components of marine ecosystem and their interactions
%B IEEE/OES Acoustics in Underwater Geosciences Symposium (RIO Acoustics)
%C Piscataway
%D 2013
%L fdi:010064376
%G ENG
%I IEEE
%@ 978-1-4799-0362-7
%K PEROU ; PACIFIQUE
%M ISI:000330575600021
%P 3
%R 10.1109/RIOAcoustics.2013.6683995
%U https://www.documentation.ird.fr/hor/fdi:010064376
%> https://www.documentation.ird.fr/intranet/publi/depot/2015-04-27/010064376.pdf
%W Horizon (IRD)
%X Here we show how routine acoustic data, primarily collected for stock assessment, allows for a 3D vision of the abiotic and biotic components of marine ecosystem and to study their interactions. Data, which can be obtained from any vessel geared with multi-frequency echosounders, provide relevant information to study the impact of physical processes on biogeochemical and ecological processes marine life and extracting valid information about the pelagic habitat and its spatial structure. All these data are to develop actual Ecosystem-based Fisheries Management in the current context of climate change. As an example we propose a synthesis of a scientific program developed in the Humboldt Current system off Peru which is the most productive in terms of fish and encompasses a shallow and intense oxygen minimum zone.
%B RIO Acoustics 2013
%8 2013/07/24-26
%$ 040 ; 036

%0 Unpublished Work
%9 AP : Autres productions
%A Habasque, Jérémie
%A Bachiri, F.
%A Ben Mhamed, A.
%A Boncoeur, J.
%A Brind'amour, A.
%A Tito de Morais, Luis
%A Weigel, Jean-Yves
%A Laë, Raymond
%T Guide d'utilisation du programme de calcul des indicateurs socioéconomiques, bioécologiques et de gouvernance des AMPs
%D 2012
%L fdi:010064455
%G FRE
%I IRD
%P 54
%U https://www.documentation.ird.fr/hor/fdi:010064455
%> https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers15-05/010064455.pdf
%W Horizon (IRD)
%X Ce manuel est destiné aux utilisateurs (gestionnaires et scientifiques) qui visent à évaluer l'efficacité bioécologique, socioéconomique et de gouvernance des AMPs. Il est donc conçu pour calculer ces trois types d'indicateurs et estimer leurs efficacités et contributions à la pondération des trois familles (biologique, socioéconomique et de gouvernance). Une interface graphique est ainsi développée pour répondre à ces besoins. L'ensemble des résultats est compilé dans des rapports .odt.
%$ 122 ; 040