@article{fdi:010086398,
  title = {{G}lobal decline of pelagic fauna in a warmer ocean},
  author = {{A}riza, {A}. and {L}engaigne, {M}atthieu and {M}enk{\`e}s, {C}hristophe and {L}ebourges {D}haussy, {A}nne and {R}eceveur, {A}. and {G}orgues, {T}homas and {H}abasque, {J}{\'e}r{\'e}mie and {G}utierrez, {M}. and {M}aury, {O}livier and {B}ertrand, {A}rnaud},
  editor = {},
  language = {{ENG}},
  abstract = {{P}elagic fauna is expected to be impacted under climate change according to ecosystem simulations. {H}owever, the direction and magnitude of the impact is still uncertain and still not corroborated by observation-based statistical studies. {H}ere 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. {W}e 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. {L}ow 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. {W}e further show that strong mitigation measures to contain global warming below 2 degrees {C} would reduce these impacts to less than half.},
  keywords = {{MONDE}},
  booktitle = {},
  journal = {{N}ature {C}limate {C}hange},
  volume = {[{E}arly access]},
  numero = {},
  pages = {[22 p.]},
  ISSN = {1758-678{X}},
  year = {2022},
  DOI = {10.1038/s41558-022-01479-2},
  URL = {https://www.documentation.ird.fr/hor/fdi:010086398},
}

@article{fdi:010086341,
  title = {{G}lobal decline of pelagic fauna in a warmer ocean},
  author = {{A}riza, {A}. and {L}engaigne, {M}atthieu and {M}enk{\`e}s, {C}hristophe and {L}ebourges {D}haussy, {A}nne and {R}eceveur, {A}. and {G}orgues, {T}homas and {H}abasque, {J}{\'e}r{\'e}mie and {G}utierrez, {M}. and {M}aury, {O}livier and {B}ertrand, {A}rnaud},
  editor = {},
  language = {{ENG}},
  abstract = {{P}elagic fauna is expected to be impacted under climate change according to ecosystem simulations. {H}owever, the direction and magnitude of the impact is still uncertain and still not corroborated by observation-based statistical studies. {H}ere 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. {W}e 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. {L}ow 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. {W}e further show that strong mitigation measures to contain global warming below 2 degrees {C} would reduce these impacts to less than half.},
  keywords = {{MONDE}},
  booktitle = {},
  journal = {{N}ature {C}limate {C}hange},
  volume = {12},
  numero = {10},
  pages = {928--934 + 15 p.},
  ISSN = {1758-678{X}},
  year = {2022},
  DOI = {10.1038/s41558-022-01479-2},
  URL = {https://www.documentation.ird.fr/hor/fdi:010086341},
}

@article{fdi:010085184,
  title = {{C}omprehensive spatial distribution of tropical fish assemblages from multifrequency acoustics and video fulfils the island mass effect framework},
  author = {{S}alvetat, {J}ulie and {B}ez, {N}icolas and {H}abasque, {J}{\'e}r{\'e}mie and {L}ebourges {D}haussy, {A}nne and {L}opes, {C}. and {R}oudaut, {G}ildas and {S}imier, {M}onique and {T}ravassos, {P}. and {V}argas, {G}. and {B}ertrand, {A}rnaud},
  editor = {},
  language = {{ENG}},
  abstract = {{T}ropical marine ecosystems are highly biodiverse and provide resources for small-scale fisheries and tourism. {H}owever, precise information on fish spatial distribution is lacking, which limits our ability to reconcile exploitation and conservation. {W}e combined acoustics to video observations to provide a comprehensive description of fish distribution in a typical tropical environment, the {F}ernando de {N}oronha {A}rchipelago ({FNA}) off {N}ortheast {B}razil. {W}e identified and classified all acoustic echoes into ten fish assemblage and two triggerfish species. {T}his opened up the possibility to relate the different spatial patterns to a series of environmental factors and the level of protection. {W}e provide the first biomass estimation of the black triggerfish {M}elichthys niger, a key tropical player. {B}y 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. {W}e also complete the portrait of the island mass effect revealing a clear spatial dissymmetry regarding fish distribution. {I}ndeed, while primary productivity is higher downstream, fish concentrate upstream. {T}he comprehensive fish distribution provided by our approach is directly usable to implement scientific-grounded {M}arine {S}patial {P}lanning.},
  keywords = {{ATLANTIQUE} ; {BRESIL} ; {ZONE} {TROPICALE} ; {FERNANDO} {DE} {NORONHA} {ARCHIPEL}},
  booktitle = {},
  journal = {{S}cientific {R}eports - {N}ature},
  volume = {12},
  numero = {1},
  pages = {8787 [24 ]},
  ISSN = {2045-2322},
  year = {2022},
  DOI = {10.1038/s41598-022-12409-9},
  URL = {https://www.documentation.ird.fr/hor/fdi:010085184},
}

@article{fdi:010083336,
  title = {{M}acrozooplankton and micronekton diversity and associated carbon vertical patterns and fluxes under distinct productive conditions around the {K}erguelen {I}slands},
  author = {{C}ott{\'e}, {C}. and {A}riza, {A}. and {B}erne, {A}. and {H}abasque, {J}{\'e}r{\'e}mie and {L}ebourges {D}haussy, {A}nne and {R}oudaut, {G}ildas and {E}spinasse, {B}. and {H}unt, {B}. {P}. {V}. and {P}akhomov, {E}. {A}. and {H}enschke, {N}. and {P}{\'e}ron, {C}. and {C}onchon, {A}. and {K}oedooder, {C}. and {I}zard, {L}. and {C}herel, {Y}.},
  editor = {},
  language = {{ENG}},
  abstract = {{M}esopelagic 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. {I}n the {S}outhern {O}cean, a prominent {H}igh {N}utrient {L}ow {C}hlorophyll ({HNLC}) and low carbon export region, the contribution of {MM} to the vertical carbon flux of the biological pump remains largely unknown. {F}urthermore, few studies have investigated {MM} communities and vertical flux in naturally iron fertilized areas associated with shallow bathymetry. {I}n this study, we assessed the {MM} community diversity, abundance and biomass in the {K}erguelen {I}sland region, including two stations in the {HNLC} region upstream of the islands, and two stations in naturally iron fertilized areas, one on the {P}lateau, and one downstream of the {P}lateau. {T}he {MM} community was examined using a combination of trawl sampling and acoustic measurements at 18 and 38 k{H}z 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. {W}hile salps ({S}alpa thompsoni) dominated the biomass at the productive {K}erguelen {P}lateau and the downstream station, they were scarce in the {HNLC} upstream area. {I}n addition, crustaceans (mainly {E}uphausia vallentini and {T}hemisto gaudichaudii) were particularly abundant over the {P}lateau, representing a large, although varying, carbon stock in the 0-500 m water layer. {M}esopelagic fish were prominent below 400 m where they formed permanent or migrant layers accounting for the main source of carbon biomass. {T}hrough these spatial and temporal sources of variability, complex patterns of the {MM} vertical distribution and associated carbon content were identified. {T}he total carbon flux mediated by migratory myctophids at the four stations was quantified. {W}hile 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.},
  keywords = {{M}acrozooplankton ; {M}icronekton ; {V}ertical patterns ; {A}ctive carbon flux ; {S}patio-temporal variability ; {S}cattering layers ; {K}erguelen {P}lateau ; {S}outhern {O}cean ; {KERGUELEN} ; {OCEAN} {AUSTRALE}},
  booktitle = {},
  journal = {{J}ournal of {M}arine {S}ystems},
  volume = {226},
  numero = {},
  pages = {103650 [18 p.]},
  ISSN = {0924-7963},
  year = {2022},
  DOI = {10.1016/j.jmarsys.2021.103650},
  URL = {https://www.documentation.ird.fr/hor/fdi:010083336},
}

@techreport{fdi:010077719,
  title = {{M}atecho user manual : version 05},
  author = {{H}abasque, {J}{\'e}r{\'e}mie and {R}oudaut, {G}ildas and {P}errot, {Y}annick and {L}ebourges-{D}haussy, {A}nne and {B}rehmer, {P}atrice},
  editor = {},
  language = {{ENG}},
  abstract = {{M}atecho is an integrated and supervised {M}atlab processing chain, which allows realizing scientific echo-sounder data treatments. {I}t 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.},
  keywords = {},
  address = {{P}louzan{\'e}},
  publisher = {{LEMAR} ; {IRD}},
  series = {},
  pages = {99  multigr.},
  year = {2020},
  URL = {https://www.documentation.ird.fr/hor/fdi:010077719},
}

@inproceedings{fdi:010078279,
  title = {{M}atecho : an open-source tool for processing fisheries acoustics data to facilitate collaborative development [r{\'e}sum{\'e} de poster]},
  author = {{P}errot, {Y}annick and {B}rehmer, {P}atrice and {H}abasque, {J}{\'e}r{\'e}mie and {R}oudaut, {G}ildas and {B}ehagle, {N}olwenn and {S}arr{\'e}, {A}. and {D}iogoul, {N}. and {L}ebourges {D}haussy, {A}nne},
  editor = {},
  language = {{ENG}},
  abstract = {{M}atecho 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. {T}he open-source initiative helps foster collaboration and technological transfer. {M}atecho supports various formats, such as the international standard format for the exchange of fisheries acoustics raw and edited data. {T}he 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. {E}cho-integration processing is executed for each depth layer and integrates their characteristics per elementary sampling unit. {S}ound 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. {M}atecho is open-source software for researchers and provides end users with a user-friendly, free executable program.},
  keywords = {{AFRIQUE} {DE} {L}'{OUEST} ; {ATLANTIQUE}},
  numero = {},
  pages = {150},
  booktitle = {{I}nternational conference {ICAWA} 2017 and 2018 : extended book of abstract : the {AWA} project : ecosystem approach to the management of fisheries and the marine environment in {W}est {A}frican waters},
  year = {2019},
  ISBN = {978-9553602-0-06},
  URL = {https://www.documentation.ird.fr/hor/fdi:010078279},
}

@article{fdi:010073782,
  title = {{M}atecho : an open-source tool for processing fisheries acoustics data},
  author = {{P}errot, {Y}annick and {B}rehmer, {P}atrice and {H}abasque, {J}{\'e}r{\'e}mie and {R}oudaut, {G}ildas and {B}ehagle, {N}olwenn and {S}arre, {A}. and {L}ebourges {D}haussy, {A}nne},
  editor = {},
  language = {{ENG}},
  abstract = {{M}atecho 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. {T}he open-source initiative helps foster collaboration and technological transfer. {M}atecho supports various formats, such as the international standard format for the exchange of fisheries acoustics raw and edited data. {T}he 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. {E}cho-integration processing is executed for each depth layer and integrates their characteristics per elementary sampling unit. {S}ound 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. {M}atecho is open-source software for researchers and provides end users with a user-friendly, free executable program.},
  keywords = {{E}cho-sounder ; {E}cho-integration ; {S}hoal ; {S}cattered layers ; {M}ulti-frequency ; {U}nderwater acoustics},
  booktitle = {},
  journal = {{A}coustics {A}ustralia},
  volume = {46},
  numero = {2},
  pages = {241--248},
  ISSN = {1839-2571},
  year = {2018},
  DOI = {10.1007/s40857-018-0135-x},
  URL = {https://www.documentation.ird.fr/hor/fdi:010073782},
}

@article{fdi:010067792,
  title = {3-{D} habitat suitability of jack mackerel {T}rachurus murphyi in the {S}outheastern {P}acific, a comprehensive study},
  author = {{B}ertrand, {A}rnaud and {H}abasque, {J}{\'e}r{\'e}mie and {H}attab, {T}. and {H}intzen, {N}. {T}. and {O}liveros-{R}amos, {R}. and {G}utierrez, {M}. and {D}emarcq, {N}. and {G}erlotto, {F}ran{\c{c}}ois},
  editor = {},
  language = {{ENG}},
  abstract = {{S}outh {P}acific jack mackerel, {T}rachurus murphyi, has an ocean-scale distribution, from the {S}outh {A}merican coastline to {N}ew {Z}ealand and {T}asmania. {T}his fish, captured by {H}umans since the {H}olocene, is nowadays heavily exploited and its population has decreased substantially since the mid-1990s. {T}he uncertainty associated to jack mackerel population structure currently hampers management. {S}everal hypotheses have been proposed from a single population up to several discrete populations. {S}till no.definitive answer was given. {D}etermining how environmental conditions drive jack mackerel distribution can provide insights on its population structure. {T}o do so, here we performed in three steps. {F}irst, we used satellite data to develop a statistical model of jack mackerel horizontal habitat suitability. {M}odel predictions based on interaction between temperature and chlorophyll-a match the observed jack mackerel distribution, even during extreme {E}l {N}ino event. {S}econd, 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. {T}hird, on the basis of the above we built a conceptual 3{D} model of jack mackerel habitat in the {S}outheastern {P}acific. {W}e reveal the presence of a low suitable habitat along the {C}hilean and {P}eruvian 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 {P}eru. {T}his 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 {P}eru. {O}n the other hand the continuity in the habitat during most of the year explains why exchanges occur. {W}e conclude that the more likely population structure for jack mackerel is a pelagic metapopulation.},
  keywords = {{PACIFIQUE} {SUD} ; {PEROU} ; {CHILI}},
  booktitle = {},
  journal = {{P}rogress in {O}ceanography},
  volume = {146},
  numero = {},
  pages = {199--211},
  ISSN = {0079-6611},
  year = {2016},
  DOI = {10.1016/j.pocean.2016.07.002},
  URL = {https://www.documentation.ird.fr/hor/fdi:010067792},
}

@inproceedings{fdi:010067832,
  title = {{M}ultifrequency acoustics measurements during the {PIRATA} {FR}25 cruise in the {E}astern {T}ropical {A}tlantic {O}cean},
  author = {{H}abasque, {J}{\'e}r{\'e}mie and {B}ourl{\`e}s, {B}ernard and {M}achu, {E}ric and {B}rehmer, {P}atrice},
  editor = {},
  language = {{ENG}},
  abstract = {},
  keywords = {{AFRIQUE} {DE} {L}'{OUEST} ; {ATLANTIQUE}},
  numero = {},
  pages = {73},
  booktitle = {{I}nternational conference {ICAWA} 2015 : extended book of abstract : the {AWA} project : ecosystem approach to the management of fisheries and the marine environment in {W}est {A}frican waters},
  year = {2016},
  ISBN = {978-9553602-0-2},
  URL = {https://www.documentation.ird.fr/hor/fdi:010067832},
}

@inproceedings{fdi:010067826,
  title = {{O}bservations of plankton communities in the {S}enegalese upwelling system},
  author = {{M}achu, {E}ric and {C}apet, {X}. and {D}onval, {A}. and {M}baye, {B}.{C}. and {H}abasque, {J}{\'e}r{\'e}mie and {L}azar, {A}. and {B}rehmer, {P}atrice},
  editor = {},
  language = {{ENG}},
  abstract = {},
  keywords = {{SENEGAL} ; {ATLANTIQUE}},
  numero = {},
  pages = {66},
  booktitle = {{I}nternational conference {ICAWA} 2015 : extended book of abstract : the {AWA} project : ecosystem approach to the management of fisheries and the marine environment in {W}est {A}frican waters},
  year = {2016},
  ISBN = {978-9553602-0-2},
  URL = {https://www.documentation.ird.fr/hor/fdi:010067826},
}

@incollection{fdi:010064376,
  title = {{R}outine acoustic data as new tools for a 3{D} vision of the abiotic and biotic components of marine ecosystem and their interactions},
  author = {{B}ertrand, {A}rnaud and {G}rados, {D}. and {H}abasque, {J}{\'e}r{\'e}mie and {F}ablet, {R}. and {B}allón, {M}. and {C}astillo, {R}. and {G}uti{\'e}rrez, {M}. and {C}haigneau, {A}lexis and {J}osse, {E}rwan and {R}oudaut, {G}ildas and {L}ebourges {D}haussy, {A}nne and {B}rehmer, {P}atrice},
  editor = {},
  language = {{ENG}},
  abstract = {{H}ere we show how routine acoustic data, primarily collected for stock assessment, allows for a 3{D} vision of the abiotic and biotic components of marine ecosystem and to study their interactions. {D}ata, 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. {A}ll these data are to develop actual {E}cosystem-based {F}isheries {M}anagement in the current context of climate change. {A}s an example we propose a synthesis of a scientific program developed in the {H}umboldt {C}urrent system off {P}eru which is the most productive in terms of fish and encompasses a shallow and intense oxygen minimum zone.},
  keywords = {{PEROU} ; {PACIFIQUE}},
  booktitle = {{IEEE}/{OES} {A}coustics in {U}nderwater {G}eosciences {S}ymposium ({RIO} {A}coustics)},
  numero = {},
  pages = {3},
  address = {{P}iscataway},
  publisher = {{IEEE}},
  series = {},
  year = {2013},
  DOI = {10.1109/{RIOA}coustics.2013.6683995},
  ISBN = {978-1-4799-0362-7},
  URL = {https://www.documentation.ird.fr/hor/fdi:010064376},
}

@techreport{fdi:010064455,
  title = {{G}uide d'utilisation du programme de calcul des indicateurs socio{\'e}conomiques, bio{\'e}cologiques et de gouvernance des {AMP}s},
  author = {{H}abasque, {J}{\'e}r{\'e}mie and {B}achiri, {F}. and {B}en {M}hamed, {A}. and {B}oncoeur, {J}. and {B}rind'amour, {A}. and {T}ito de {M}orais, {L}uis and {W}eigel, {J}ean-{Y}ves and {L}a{\¨e}, {R}aymond},
  editor = {},
  language = {{FRE}},
  abstract = {{C}e manuel est destin{\'e} aux utilisateurs (gestionnaires et scientifiques) qui visent {\`a} {\'e}valuer l'efficacit{\'e} bio{\'e}cologique, socio{\'e}conomique et de gouvernance des {AMP}s. {I}l est donc con{\c{c}}u pour calculer ces trois types d'indicateurs et estimer leurs efficacit{\'e}s et contributions {\`a} la pond{\'e}ration des trois familles (biologique, socio{\'e}conomique et de gouvernance). {U}ne interface graphique est ainsi d{\'e}velopp{\'e}e pour r{\'e}pondre {\`a} ces besoins. {L}'ensemble des r{\'e}sultats est compil{\'e} dans des rapports .odt.},
  keywords = {},
  address = {},
  publisher = {{IRD}},
  series = {},
  pages = {54},
  year = {2012},
  URL = {https://www.documentation.ird.fr/hor/fdi:010064455},
}