, Les indices ont été calculés sur la donnée brute non nettoyée. Les phases de pleine lune (PL) sont indiquées. Les valeurs de SPL sont en dBrms re 1?Pa, les autres indices sont sans unité. La couleur du cartouche indique la température de l'eau telle qu'estimée par la NOAA pour chaque mois, Variabilité des 6 indices écoacoustiques entre le 29 avril 2018 et le 4 février 2019

, Spectrogramme d'un échantillon de 5 min enregistré par la station fixe d'Europa. L'échantillon de son correspondant est disponible dans le supplément électronique de la thèse : E24_EUR10fixe_annexe6.4_020918_121228.wav. Plusieurs évènements de broutage par les poissons perroquets sont clairement audibles entre 2min45 et 3min30

. Towsey, En effet dans le cas d'Europa, chaque site de suivi est en général échantillonné durant une plongée de 1 h tous les 3 à 5 ans, il est ainsi difficile de savoir si l'observation de changements de la structure des communautés d'organismes mobiles (e.g. poissons) est due au moment où est réalisé l'échantillonnage ou à une réelle transformation de l'écosystème. Les résultats du chapitre 6 ont montré la pertinence des indices écoacoustiques pour suivre les grandes tendances de l'activité biologique du récif. Ces indices pourraient être combinés pour produire des « long-term false color spectrogram », afin de fournir aux gestionnaires une visualisation rapide et synthétique des variations temporelles à long-terme des paysages sonores, les résultats des suivis réalisés in situ dans un contexte temporel, 2014.

, Cependant, la réponse à certains objectifs de gestion, ou certains questionnements scientifiques, peut nécessiter une information différente de celle fournie par les indices écoacoustiques. Des méthodes de détection automatique pourraient alors être employées. J'envisage prochainement de tester quelques-unes de ces approches pour évaluer leur

&. Clink and . Klinck, indiquent en effet que la diversité des types de signaux et des environnements acoustiques nécessitent de tester plusieurs méthodes de classification pour déterminer la plus adaptée à chaque cas. Une première étape pourrait être d'utiliser une méthode de classification non, 2018.

, Multiresolution Analysis of Acoustic Diversity -MAAD

. Ulloa, Une deuxième étape pourrait se focaliser sur certains signaux d'origine biologique mis en évidence dans la première étape. Il s'agirait alors de les détecter de façon automatique dans le jeu de données en utilisant des méthodes de machine learning basée sur de la classification supervisée, ) afin d'identifier les principaux types de signaux présents dans le jeu de données (i.e. les 11 mois de suivis temporel à Europa), 2017.

. Katz, Un jeu de données (« training dataset ») a été constitué à partir d'annotations manuelles pour entraîner le système de détection à reconnaître automatiquement les évènements annotés par recherche d'analogies avec les templates (« cross correlation »). Le système est ensuite validé sur un deuxième jeu de données de taille équivalente (« validation dataset ») également constitué à partir d'annotations manuelles. Ce deuxième jeu de données a pour but de vérifier la capacité de détection du système. Une fois identifiés les paramètres du système qui optimisent la capacité de détection, nous l'utiliserons sur le jeu de données complet (i.e. les 11 mois de suivis temporel à Europa) afin d'explorer la phénologie de l'activité de broutage sur ce récif et vérifier la cohérence des résultats par rapport à la littérature. Le suivi en « quasi temps réel » de ce processus particulièrement clé dans un contexte de changements climatiques, les derniers mois visant à mettre au point un détecteur automatique permettant de quantifier l'activité de broutage par les poissons perroquets. Nous travaillons avec le package « monitoR, 2014.

. Kittinger, articuler l'utilisation de cette méthode avec les autres outils de suivis, l'adaptation du suivi des écosystèmes coralliens à un monde qui change rapidement est en bonne voie. D'autre défis nous attendent, à commencer par la prise en compte des spécificités socioécologiques locales, incontournable dans le succès des stratégies de conservation que nous devons mettre en oeuvre, 2012.

. Hoegh-guldberg, Cette prise en compte implique la recherche des leviers de conservation adaptés à chaque situation (e.g. interdictions saisonnières de la pêche de certaines espèces, ou de certains engins de pêche, ou de certaines zones, tailles minimales de captures), en s'appuyant sur la perception des bénéfices par les populations locales, 2012.

A. , Cependant, les récents progrès technologiques (e.g. véhicules autonomes sous-marins, stimulation de la croissance de boutures de corail par courant faible, sélection génétiques de boutures thermo-résistantes, Doropoulos et al., 2019) et seront certainement multipliées dans les prochaines années. Comme pour les méthodes de suivis, les technologies dont nous disposons aujourd'hui, 2012.

D. A. Abraham, Underwater Acoustic Signal Processing, 2019.

M. A. Acevedo and L. J. Villanueva-rivera, Using Automated Digital Recording Systems as Effective Tools for the Monitoring of Birds and Amphibians, vol.34, pp.211-214, 2006.

M. A. Acevedo, C. J. Corrada-bravo, H. Corrada-bravo, L. J. Villanueva-rivera, and T. M. Aide, Automated classification of bird and amphibian calls using machine learning: A comparison of methods, Ecological Informatics, vol.4, issue.4, pp.206-214, 2009.

Y. Afeworki, J. J. Videler, and J. H. Bruggemann, Seasonally changing habitat use patterns among roving herbivorous fishes in the southern Red Sea: The role of temperature and algal community structure, Coral Reefs, vol.32, issue.2, pp.475-485, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00909858

T. M. Aide, C. Corrada-bravo, M. Campos-cerqueira, C. Milan, G. Vega et al., Realtime bioacoustics monitoring and automated species identification, PeerJ, vol.1, 2013.

M. C. Amorim and A. D. Hawkins, Ontogeny of acoustic and feeding behaviour in the grey gurnard, Eutrigla gurnardus. Ethology, vol.111, issue.3, pp.255-269, 2005.

M. C. Amorim, Communication in Fishes: Diversity of Sound Production in Fish. Communication in Fishes, pp.71-105, 2006.

S. Andréfouët, G. Cabioch, B. Flamand, and B. Pelletier, A reappraisal of the diversity of geomorphological and genetic processes of New Caledonian coral reefs: a synthesis from optical remote sensing, coring and acoustic multibeam observations, Coral Reefs, vol.28, issue.3, pp.691-707, 2009.

A. Anker, S. T. Ahyong, P. Y. Noël, and A. R. Palmer, Morphological Phylogeny of Alpheid Shrimps: Parallel Preadaptation and the Origin of a Key Morphological Innovation, the Snapping Claw, Evolution, vol.60, issue.12, p.2507, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00132966

K. Anthony, L. K. Bay, R. Costanza, J. Firn, J. Gunn et al., New interventions are needed to save coral reefs, Nature Ecology and Evolution, vol.1, issue.10, pp.1420-1422, 2017.

W. W. Au and K. Banks, The acoustics of snapping shrimps, The Journal of the Acoustical Society of America, vol.101, issue.5, pp.3032-3032, 1998.

W. W. Au and M. C. Hastings, Principles of marine bioacoustics, 2008.

T. Bajjouk, P. Mouquet, M. Ropert, J. P. Quod, L. Hoarau et al., Detection of changes in shallow coral reefs status: Towards a spatial approach using hyperspectral and multispectral data, Ecological Indicators, vol.96, pp.174-191, 2019.
URL : https://hal.archives-ouvertes.fr/hal-01906870

D. R. Barneche, E. L. Rezende, V. Parravicini, E. Maire, G. J. Edgar et al., Body size, reef area and temperature predict global reef-fish species richness across spatial scales, Global Ecology and Biogeography, vol.28, issue.3, pp.315-327, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02403252

A. D. Barnosky, N. Matzke, S. Tomiya, G. O. Wogan, B. Swartz et al., Has the Earth's sixth mass extinction already arrived?, Nature, vol.471, issue.7336, pp.51-57, 2011.

J. Bascompte, C. J. Melián, and E. Sala, Interaction strength combinations and the overfishing, Proceedings of the National Academy of Sciences of the United States of America, vol.102, pp.5443-5447, 2005.

E. Bayraktarov, M. I. Saunders, S. Abdullah, M. Mills, J. Beher et al., The cost and feasibility of marine coastal restoration, Ecological Applications, vol.26, issue.4, pp.1055-1074, 2016.

C. Bedoya, C. Isaza, J. M. Daza, and J. D. López, Automatic identification of rainfall in acoustic recordings, Ecological Indicators, vol.75, pp.95-100, 2017.

D. R. Bellwood, T. P. Hughes, and A. S. Hoey, Sleeping Functional Group Drives Coral-Reef Recovery, Current Biology, vol.16, issue.24, pp.2434-2439, 2006.

D. R. Bellwood, A. S. Hoey, and T. P. Hughes, Human activity selectively impacts the ecosystem roles of parrotfishes on coral reefs, Proceedings of the Royal Society B: Biological Sciences, vol.279, pp.1621-1629, 1733.

D. R. Bellwood, R. P. Streit, S. J. Brandl, and S. B. Tebbett, The meaning of the term 'function' in ecology: A coral reef perspective, Functional Ecology, vol.33, pp.948-961, 2019.

D. R. Bellwood, M. S. Pratchett, T. H. Morrison, G. G. Gurney, T. P. Hughes et al., Coral reef conservation in the Anthropocene: Confronting spatial mismatches and prioritizing functions, Biological Conservation, 2019.

F. Bertucci, E. Parmentier, L. Berten, R. M. Brooker, and D. Lecchini, Temporal and spatial comparisons of underwater sound signatures of different reef habitats in Moorea Island, French Polynesia, PLoS ONE, vol.10, issue.9, pp.1-12, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01211705

F. Bertucci, E. Parmentier, G. Lecellier, A. D. Hawkins, D. Lecchini et al., Acoustic indices provide information on the status of coral reefs: an example from Moorea Island in the South Pacific, Scientific Reports, vol.6, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01370610

F. Bertucci, E. Parmentier, C. Berthe, and M. Besson, Snapshot recordings provide a first description of the acoustic signatures of deeper habitats adjacent to coral reefs of Moorea, PeerJ, vol.5, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01654685

H. L. Beyer, E. V. Kennedy, M. Beger, C. A. Chen, J. E. Cinner et al., Risk-sensitive planning for conserving coral reefs under rapid climate change. Conservation Letters, e12587, 2018.

L. Bigot, H. Bruggemann, C. Cadet, B. Cauvin, P. Chabanet et al., Point 1 du suivi de « l'effet réserve » sur les communautés ichtyologiques et benthiques récifales -Secteurs de St Gilles/La Saline et de Saint-Leu -Etat des lieux à 7 ans après la création de la Réserve Naturelle Nationale Marine de La Réunion, pp.39-50, 2016.

L. Bittencourt, M. Barbosa, E. Secchi, J. Lailson-brito, and A. Azevedo, Acoustic Habitat of an Oceanic Archipelago in the Southwestern Atlantic. Deep-Sea Research Part I, vol.115, pp.103-111, 2016.

. Blue-marble-geographics, Global Mapper: Release 19, 2018.

D. T. Blumstein, D. J. Mennill, P. Clemins, L. Girod, K. Yao et al., Acoustic monitoring in terrestrial environments using microphone arrays: Applications, technological considerations and prospectus, Journal of Applied Ecology, vol.48, issue.3, pp.758-767, 2011.

N. T. Boelman, G. P. Asner, P. J. Hart, and R. E. Martin, Multi-trophic invasion resistance in Hawaii: Bioacoustics, field surveys, and airborne remote sensing, Ecological Applications, vol.17, issue.8, pp.2137-2144, 2007.

D. R. Bohnenstiehl, A. Lillis, and D. B. Eggleston, The Curious Acoustic Behavior of Estuarine Snapping Shrimp: Temporal Patterns of Snapping Shrimp Sound in Sub-Tidal Oyster Reef Habitat, PloS One, vol.11, issue.1, p.143691, 2016.

D. R. Bohnenstiehl, R. P. Lyon, O. N. Caretti, S. W. Ricci, and D. B. Eggleston, Investigating the utility of ecoacoustic metrics in marine soundscapes, Journal of Ecoacoustics, vol.2, p.1156, 2018.

J. A. Bohnsack and S. P. Bannerot, A Stationary Visual Census Technique for Quantitatively Assessing Community Structure of Coral Reef Fishes, NOAA Technical Report NMFS, vol.41, pp.1-15, 1986.

M. Bolgan, M. C. Amorim, P. J. Fonseca, L. Di-iorio, and E. Parmentier, Acoustic complexity of vocal fish communities: A field and controlled validation, Scientific Reports, vol.8, issue.1, 2018.

G. Boussarie, J. Bakker, O. S. Wangensteen, S. Mariani, L. Bonnin et al., , 2018.

, Environmental DNA illuminates the dark diversity of sharks, Science Advances, vol.4, issue.5

T. Bradfer-lawrence, N. Gardner, L. Bunnefeld, N. Bunnefeld, S. G. Willis et al., Guidelines for the use of acoustic indices in environmental research, Methods in Ecology and Evolution, vol.10, pp.1796-1807, 2019.

S. J. Brandl, L. Tornabene, C. H. Goatley, J. M. Casey, R. A. Morais et al., Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning, Science, vol.364, issue.6446, pp.1189-1192, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02432315

F. Bretz, P. Westfall, R. M. Heiberger, A. Schuetzenmeister, and S. Scheibe, R Package 'multcomp, 2017.

V. E. Brock, A preliminary report on a method of estimating reef fish populations, Journal of Wildlife Management, vol.18, pp.297-308, 1954.

R. E. Brock, A critique of the visual census method for assessing coral reef fish populations, Bulletin of Marine Science, vol.32, pp.269-276, 1982.

E. Browning, R. Gibb, P. Glover-kapfer, and K. E. Jones, Passive acoustic monitoring in ecology and conservation, WWF Conservation Technology Series, vol.1, issue.2, pp.1-75, 2017.

G. Buscaino, M. Ceraulo, N. Pieretti, V. Corrias, A. Farina et al., Temporal patterns in the soundscape of the shallow waters of a Mediterranean marine protected area, Scientific Reports, vol.6, p.34230, 2016.

J. H. Burns, D. Delparte, R. D. Gates, and M. Takabayashi, Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs, PeerJ, vol.3, 2015.

R. T. Buxton, M. F. Mckenna, M. Clapp, E. Meyer, E. Stabenau et al., Efficacy of extracting indices from large-scale acoustic recordings to monitor biodiversity, Conservation Biology, vol.32, issue.5, pp.1174-1184, 2018.

B. J. Cardinale, J. E. Duffy, A. Gonzalez, D. U. Hooper, C. Perrings et al., Corrigendum: Biodiversity loss and its impact on humanity, Nature, vol.489, issue.7415, pp.326-326, 2012.

D. H. Cato and M. J. Bell, Ultrasonic ambient noise in Australian shallow waters at frequencies up to 200 kHz (No. MRL-TR-91-23), Materials Research Labs, 1992.

D. H. Cato and R. D. Mccauley, Australian research in ambient sea noise, Acoustics Australia, vol.30, issue.1, pp.13-20, 2002.

M. Ceraulo, E. Papale, F. Caruso, F. Filiciotto, R. Grammauta et al., Acoustic comparison of a patchy Mediterranean shallow water seascape: Posidonia oceanica meadow and sandy bottom habitats, Ecological Indicators, vol.85, pp.1030-1043, 2018.

P. Chabanet, L. Bigot, J. B. Nicet, P. Durville, L. Massé et al., Coral reef monitoring in the Iles Eparses, vol.72, pp.62-71, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01908214

A. J. Cheal, M. A. Macneil, M. J. Emslie, and H. Sweatman, The threat to coral reefs from more intense cyclones under climate change, Global Change Biology, vol.23, issue.4, pp.1511-1524, 2017.

J. E. Cinner, C. Huchery, E. S. Darling, A. T. Humphries, N. A. Graham et al., Evaluating social and ecological vulnerability of coral reef fisheries to climate change, PloS One, vol.8, issue.9, 2013.

J. E. Cinner, E. Maire, C. Huchery, M. A. Macneil, N. A. Graham et al., Gravity of human impacts mediates coral reef conservation gains, Proceedings of the National Academy of Sciences of the United States of America, vol.115, pp.6116-6125, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01824520

D. J. Clink and H. Klinck, GIBBONR: An R package for the detection and classification of acoustic signals using machine learning, 2018.

E. Clua, P. Legendre, L. Vigliola, F. Magron, M. Kulbicki et al., Medium scale approach (MSA) for improved assessment of coral reef fish habitat, Journal of Experimental Marine Biology and Ecology, vol.333, pp.219-230, 2006.

K. R. Curtis, B. M. Howe, and J. A. Mercer, Low-frequency ambient sound in the North Pacific: Long time series observations, The Journal of the Acoustical Society of America, vol.106, issue.6, pp.3189-3200, 1999.

S. Mouillot, D. Kulbicki, M. Andréfouët, S. Bellwood, D. R. Cinner et al., Human-mediated loss of phylogenetic and functional diversity in coral reef fishes, Current Biology, vol.24, pp.555-560, 2014.

S. Mouillot, D. Wantiez, L. Friedlander, A. M. Kulbicki, M. Vigliola et al., Marine reserves lag behind wilderness in the conservation of key functional roles, Nature Communication, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01925268

E. S. Darling, L. Alvarez-filip, T. A. Oliver, T. R. Mcclanahan, and I. M. Côté, Evaluating life-history strategies of reef corals from species traits, Ecology Letters, vol.15, issue.12, pp.1378-1386, 2012.

E. S. Darling, N. A. Graham, F. A. Januchowski-hartley, K. L. Nash, M. S. Pratchett et al., Relationships between structural complexity, coral traits, and reef fish assemblages, Coral Reefs, vol.36, issue.2, pp.561-575, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01927918

M. Depraetere, S. Pavoine, F. Jiguet, A. Gasc, S. Duvail et al., Monitoring animal diversity using acoustic indices: Implementation in a temperate woodland, Ecological Indicators, vol.13, issue.1, pp.46-54, 2012.
URL : https://hal.archives-ouvertes.fr/ird-02149907

C. Desjonquères, F. Rybak, M. Depraetere, A. Gasc, I. Le-viol et al., First description of underwater acoustic diversity in three temperate ponds, PeerJ, vol.3, 2015.

C. Doropoulos, F. Vons, J. Elzinga, R. Ter-hofstede, K. Salee et al., Testing Industrial-Scale Coral Restoration Techniques: Harvesting and Culturing Wild Coral-Spawn Slicks, Frontiers in Marine Science, vol.6, p.658, 2019.

. Dosits, University of Rhode Island, 2019.

G. J. Edgar, R. D. Stuart-smith, T. J. Willis, S. Kininmonth, S. C. Baker et al., Global conservation outcomes depend on marine protected areas with five key features, Nature, vol.506, issue.7487, pp.216-220, 2014.

S. Elise and J. H. Bruggemann, Rapport de campagne CORCOPA, vol.51, p.pp, 2018.

E. S. Bruggemann and J. H. , Etat acoustique de référence des récifs coralliens de l'île Europa et premiers résultats du suivi acoustique continu d'avril 2018 à février 2019, vol.55, p.pp, 2019.

S. Elise, A. Bailly, I. Urbina-barreto, G. Mou-tham, F. Chiroleu et al., An optimised passive acoustic sampling scheme to discriminate among coral reefs' ecological states, Ecological Indicators, 2019.

S. Elise, I. Urbina-barreto, R. Pinel, V. Mahamadaly, S. Bureau et al., Assessing key ecosystem functions through soundscapes: a new perspective from coral reefs, Ecological Indicators, 2019.

C. D. Elvidge, J. B. Dietz, R. Berkelmans, S. Andrefouet, W. Skirving et al., Satellite observation of Keppel Islands (Great Barrier Reef) 2002 coral bleaching using IKONOS data, Coral Reefs, vol.23, issue.1, pp.123-132, 2004.

M. J. Emslie, A. J. Cheal, M. A. Macneil, I. R. Miller, and H. P. Sweatman, Reef fish communities are spooked by scuba surveys and may take hours to recover, PeerJ, vol.6, 2018.

I. C. Enochs, L. T. Toth, V. W. Brandtneris, J. C. Afflerbach, and D. P. Manzello, Environmental determinants of motile cryptofauna on an eastern Pacific coral reef, Marine Ecology Progress Series, vol.438, pp.105-118, 2011.

C. Erbe, Underwater acoustics: noise and the effects on marine mammals, A Pocket Handbook, vol.164, 2011.

. Esri, ArcGIS Desktop: Release 10, 2018.

F. A. Everest, R. W. Yound, and M. W. Johnson, Acoustical characteristics of noise produced by snapping shrimp, The Journal of the Acoustical Society of America, vol.20, pp.137-142, 1948.

M. Facon, M. Pinault, D. Obura, S. Pioch, K. Pothin et al., A comparative study of the accuracy and effectiveness of Line and Point Intercept Transect methods for coral reef monitoring in the southwestern Indian Ocean islands, Ecological Indicators, vol.60, pp.1045-1055, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01211778

A. Farina, Perspectives in ecoacoustics: A contribution to defining a discipline, Journal of Ecoacoustics, vol.2, 2018.

R. Ferrari, D. Mckinnon, H. He, R. N. Smith, P. Corke et al., Quantifying multiscale habitat structural complexity: A cost-effective framework for underwater 3D modelling, Remote Sensing, vol.8, issue.2, 2016.

L. M. Ferreira, E. G. Oliveira, L. C. Lopes, M. R. Brito, J. Baumgarten et al., What do insects, anurans, birds, and mammals have to say about soundscape indices in a tropical savanna, Journal of Ecoacoustics, vol.2, p.6, 2018.

. Fishbase, , 2019.

F. P. Fischer, U. Schulz, H. Schubert, P. Knapp, and M. Schmöger, Quantitative assessment of grassland quality: acoustic determination of population sizes of orthopteran indicator species, Ecological Applications, vol.7, issue.3, pp.909-920, 1997.

R. Fisher, R. A. O'leary, S. Low-choy, K. Mengersen, N. Knowlton et al., Species richness on coral reefs and the pursuit of convergent global estimates, Current Biology, vol.25, issue.4, pp.500-505, 2015.

K. E. Frasier, M. A. Roch, M. S. Soldevilla, S. M. Wiggins, L. P. Garrison et al., Automated classification of dolphin echolocation click types from the Gulf of Mexico, PLoS Computational Biology, vol.13, issue.12, pp.1-23, 2017.

S. E. Freeman, M. J. Buckingham, L. A. Freeman, M. O. Lammers, and G. L. Spain, Crosscorrelation, triangulation, and curved-wavefront focusing of coral reef sound using a bi-linear hydrophone array, The Journal of the Acoustical Society of America, vol.137, issue.1, p.30, 2014.

S. E. Freeman, F. L. Rohwer, G. L. D'spain, A. M. Friedlander, A. K. Gregg et al., The origins of ambient biological sound from coral reef ecosystems in the Line Islands archipelago, The Journal of the Acoustical Society of America, vol.135, issue.4, pp.1775-1788, 2014.

L. A. Freeman and S. E. Freeman, Rapidly obtained ecosystem indicators from coral reef soundscapes, Marine Ecology Progress Series, vol.561, pp.69-82, 2016.

S. E. Freeman, L. A. Freeman, G. Giorli, and A. F. Haas, Photosynthesis by marine algae produces sound, contributing to the daytime soundscape on coral reefs, Plos One, vol.13, issue.10, pp.1-14, 2018.

A. M. Friedlander, E. K. Brown, P. L. Jokiel, W. R. Smith, and K. S. Rodgers, Effects of habitat, wave exposure, and marine protected area status on coral reef fish assemblages in the Hawaiian archipelago, Coral Reefs, vol.22, issue.3, pp.291-305, 2003.

K. Frieler, M. Meinshausen, A. Golly, M. Mengel, K. Lebek et al., Limiting global warming to 2 C is unlikely to save most coral reefs, Nature Climate Change, vol.3, issue.2, p.165, 2013.

S. Fuller, A. C. Axel, D. Tucker, and S. H. Gage, Connecting soundscape to landscape: Which acoustic index best describes landscape configuration? Ecological Indicators, vol.58, pp.207-215, 2015.

C. J. Fulton, R. A. Abesamis, C. Berkström, M. Depczynski, N. J. Graham et al.,

P. Tinkler, Form and function of tropical macroalgal reefs in the Anthropocene, Functional Ecology, 2019.

A. Gasc, J. Sueur, S. Pavoine, R. Pellens, and P. Grandcolas, Biodiversity sampling using a global acoustic approach: contrasting sites with microendemics in New Caledonia, PLoS ONE, vol.8, p.65311, 2013.

A. Gasc, D. Francomano, J. B. Dunning, and B. C. Pijanowski, Future directions for soundscape ecology: The importance of ornithological contributions, The Auk, vol.134, issue.1, pp.215-228, 2017.

R. Gibb, E. Browning, P. Glover-kapfer, and K. E. Jones, Emerging opportunities and challenges for passive acoustics in ecological assessment and monitoring, Methods in Ecology and Evolution, vol.10, issue.2, pp.169-185, 2019.

W. E. Gómez, C. V. Isaza, and J. M. Daza, Identifying disturbed habitats: A new method from acoustic indices, Ecological Informatics, vol.45, pp.16-25, 2018.

F. J. González-barrios and L. Álvarez-filip, A framework for measuring coral species-specific contribution to reef functioning in the Caribbean, Ecological Indicators, vol.95, pp.877-886, 2018.

N. A. Graham and K. L. Nash, The importance of structural complexity in coral reef ecosystems, Coral Reefs, vol.32, issue.2, pp.315-326, 2013.

N. A. Graham, S. Jennings, M. A. Macneil, D. Mouillot, and S. K. Wilson, Predicting climatedriven regime shifts versus rebound potential in coral reefs, Nature, vol.518, issue.7537, pp.94-97, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01841302

N. A. Graham and T. R. Mcclanahan, The Last Call for Marine Wilderness ?, BioScience, vol.63, issue.5, pp.397-402, 2013.

A. L. Green and D. R. Bellwood, Monitoring functional groups of herbivorous reef fishes as indicators of coral reef resilience -A practical guide for coral reef managers in the Asia Pacific region, 2009.

S. J. Green, N. K. Dulvy, A. M. Brooks, J. L. Akins, A. B. Cooper et al., Linking removal targets to the ecological effects of invaders: a predictive model and field test, Ecological Applications, vol.24, issue.6, pp.1311-1322, 2014.

M. L. Groner, J. Maynard, R. Breyta, R. B. Carnegie, A. Dobson et al., Managing marine disease emergencies in an era of rapid change, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.371, 1689.
URL : https://hal.archives-ouvertes.fr/hal-01282464

N. Guillemot, M. Kulbicki, P. Chabanet, and L. Vigliola, Functional redundancy patterns reveal non-random assembly rules in a species-rich marine assemblage, PLoS ONE, issue.10, p.6, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02647484

,

W. M. Hamner, P. L. Colin, and P. P. Hamner, Export-import dynamics of zooplankton on a coral reef in Palau, Marine Ecology Progress Series, vol.334, pp.83-92, 2007.

A. R. Harborne, A. Rogers, Y. Bozec, and P. J. Mumby, Multiple Stressors and the Functioning of Coral Reefs, Annual Review of Marine Science, vol.9, pp.445-468, 2016.

D. L. Harris, A. Rovere, E. Casella, H. Power, R. Canavesio et al., Coral reef structural complexity provides important coastal protection from waves under rising sea levels, Science Advances, vol.4, issue.2, pp.1-8, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01724281

S. A. Harris, N. T. Shears, and C. A. Radford, Ecoacoustic indices as proxies for biodiversity on temperate reefs, Methods in Ecology and Evolution, vol.7, issue.6, pp.713-724, 2016.

W. M. Hartmann, H. Klinck, S. L. Nieukirk, H. Matsumoto, R. P. Dziak et al., The not-sosilent world: Measuring Arctic, Equatorial , and Antarctic soundscapes in the Atlantic Ocean. Deep-Sea Research Part I, vol.122, pp.95-104, 1998.

J. D. Hedley, C. M. Roelfsema, I. Chollett, A. R. Harborne, S. F. Heron et al., Remote sensing of coral reefs for monitoring and management: A review, Remote Sensing, vol.8, issue.2, 2016.

H. L. Heenehan, M. Parijs, . Van, L. Bejder, J. A. Tyne et al., Natural and anthropogenic events influence the soundscapes of four bays on Hawaii Island, Marine Pollution Bulletin, vol.124, pp.9-20, 2017.

J. A. Hildebrand, Anthropogenic and natural sources of ambient noise in the ocean, Marine Ecology Progress Series, vol.395, pp.5-20, 2009.

O. Hoegh-guldberg, E. V. Kennedy, H. L. Beyer, C. Mcclennen, and H. P. Possingham, Securing a long-term future for coral reefs, Trends in Ecology & Evolution, vol.12, issue.12, pp.936-944, 2018.

S. H. Holles, S. D. Simpson, A. N. Radford, L. Berten, and D. Lecchini, Boat noise disrupts orientation behaviour in a coral reef fish, Marine Ecology Progress Series, vol.485, pp.295-300, 2013.

S. J. Hughes, D. D. Ellis, D. M. Chapman, and P. R. Staal, Low-frequency acoustic propagation loss in shallow water over hard-rock seabeds covered by a thin layer of elastic-solid sediment, The Journal of the Acoustical Society of America, vol.88, issue.1, pp.283-297, 1990.

T. P. Hughes, D. R. Bellwood, and S. R. Connolly, Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs, Ecology Letters, vol.5, issue.6, pp.775-784, 2002.

T. P. Hughes, M. J. Rodrigues, D. R. Bellwood, D. Ceccarelli, O. Hoegh-guldberg et al., Phase Shifts, Herbivory, and the Resilience of Coral Reefs to Climate Change, Current Biology, vol.17, pp.360-365, 2007.

T. P. Hughes, M. L. Barnes, D. R. Bellwood, J. E. Cinner, G. S. Cumming et al., Coral reefs in the Anthropocene, Nature, vol.546, issue.7656, pp.82-90, 2017.

K. M. Hultgren and J. E. Duffy, Sponge host characteristics shape the community structure of their shrimp associates, Marine Ecology Progress Series, vol.407, pp.1-12, 2010.

A. K. Ibrahim, L. M. Chérubin, H. Zhuang, M. T. Schärer-umpierre, F. Dalgleish et al.,

A. Dalgleish, An approach for automatic classification of grouper vocalizations with passive acoustic monitoring, The Journal of the Acoustical Society of America, vol.143, issue.2, pp.666-676, 2018.

J. A. Idjadi and P. J. Edmunds, Scleractinian corals as facilitators for other invertebrates on a Caribbean reef, Marine Ecology Progress Series, vol.319, pp.117-127, 2006.

. Ipbes, Summary for policymakers of the global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on, IPBES secretariat, p.204, 2019.

Y. Jézéquel, J. Bonnel, J. Coston-guarini, and L. Chauvaud, Revisiting the bioacoustics of European spiny lobsters Palinurus elephas: Comparison of antennal RASPs in tanks and in situ, Marine Ecology Progress Series, vol.615, pp.143-157, 2019.

M. W. Johnson, F. A. Everest, and R. W. Young, The role of snapping shrimp (Crangon and Synalpheus) in the production of underwater noise in the sea, The Biological Bulletin, vol.93, issue.2, pp.122-138, 1947.

J. B. Juhel, Base de référence, impacts anthropiques et mesures de protection pour les requins récifaux de Nouvelle-Calédonie, 2016.

M. B. Kaplan and T. A. Mooney, Ambient noise and temporal patterns of boat activity in the US Virgin Islands National Park, Marine Pollution Bulletin, vol.98, issue.1-2, pp.221-228, 2015.

M. B. Kaplan, T. A. Mooney, J. Partan, and A. R. Solow, Coral reef species assemblages are associated with ambient soundscapes, Marine Ecology Progress Series, vol.533, pp.93-107, 2015.

M. B. Kaplan, M. O. Lammers, E. Zang, and T. A. Mooney, Acoustic and biological trends on coral reefs off, Coral Reefs, vol.37, issue.1, pp.121-133, 2017.

J. Katz, S. D. Hafner, and T. Donovan, Tools for automated acoustic monitoring within the R package monitoR, Bioacoustics, vol.25, issue.2, pp.197-210, 2016.

E. V. Kennedy, M. W. Holderied, J. M. Mair, H. M. Guzman, and S. D. Simpson, Spatial patterns in reef-generated noise relate to habitats and communities: Evidence from a Panamanian case study, Journal of Experimental Marine Biology and Ecology, vol.395, issue.1-2, pp.85-92, 2010.

E. V. Kennedy, C. T. Perry, P. R. Halloran, R. Iglesias-prieto, C. H. Schönberg et al., Avoiding coral reef functional collapse requires local and global action, Current Biology, vol.23, issue.10, pp.912-918, 2013.

J. N. Kittinger, E. M. Finkbeiner, E. W. Glazier, and L. B. Crowder, Human dimensions of coral reef social-ecological systems, Ecology and Society, vol.17, issue.4, 2012.

N. Knowlton, R. E. Brainard, R. Fisher, M. Moews, L. Plaisance et al., Coral Reef Biodiversity. Life in the World's Oceans: Diversity, Distribution, and Abundance, pp.65-78, 2010.

V. O. Knudsen, R. S. Alford, and J. W. Emling, Underwater ambient noise, Journal of Marine Research, vol.7, pp.410-429, 1948.

B. Krause and A. Farina, Using ecoacoustic methods to survey the impacts of climate change on biodiversity, Biological Conservation, vol.195, pp.245-254, 2016.

M. Kulbicki, Influence the Results Obtained From Visual Censuses, Journal of Experimental Marine Biology and Ecology, vol.222, pp.11-30, 1998.

M. Kulbicki, V. Parravicini, D. R. Bellwood, E. Arias-gonzàlez, P. Chabanet et al., Global biogeography of reef fishes: A hierarchical quantitative delineation of regions, PLoS ONE, vol.8, issue.12, 2013.

M. Kulbicki and S. Sarramégna, Comparison of density estimates derived from strip transect and distance sampling for underwater visual censuses: A case study of Chaetodontidae and Pomacanthidae, Aquatic Living Resources, vol.12, issue.5, pp.116-119, 1999.

M. Kulbicki, V. Parravicini, and D. Mouillot, Patterns and processes in reef fish body size, Ecology of fishes on coral reefs, Mora, C. (ed), pp.104-105, 2015.

W. A. Kuperman, Propagation effects associated with ambient noise. In: Sea surface sound: natural mechanisms of surface generated noise in the ocean, pp.253-272, 1988.

P. Labrosse, M. Kulbicki, and J. Ferraris, Underwater visual fish census surveys. Secretariat of the Pacific Community, p.60, 2002.

M. O. Lammers, R. E. Brainard, W. W. Au, T. A. Mooney, and K. B. Wong, An ecological acoustic recorder (EAR) for long-term monitoring of biological and anthropogenic sounds on coral reefs and other marine habitats, The Journal of the Acoustical Society of America, vol.123, issue.3, pp.1720-1728, 2008.

M. O. Lammers and L. M. Munger, From shrimp to whales: biological applications of Passive Acoustic Monitoring on a remote Pacific coral reef, Listening in the Ocean, pp.61-81, 2016.

P. Legendre, Studying Beta Diversity: Ecological Variation Partitioning By Multiple Regression and Canonical Analysis, Chinese Journal of Plant Ecology, vol.31, pp.976-981, 2007.

S. Li, H. Wu, Y. Xu, C. Peng, L. Fang et al., Mid-to high-frequency noise from high-speed boats and its potential impacts on humpback dolphins, The Journal of the Acoustical Society of America, vol.138, issue.2, pp.942-952, 2015.

U. Ligges, S. Krey, O. Mersmann, and S. Schnackenberg, tuneR: Analysis of Music and Speech, 2018.

A. Lillis, D. B. Eggleston, and D. R. Bohnenstiehl, Estuarine soundscapes: Distinct acoustic characteristics of oyster reefs compared to soft-bottom habitats, Marine Ecology Progress Series, vol.505, pp.1-17, 2014.

A. Lillis and T. A. Mooney, Snapping shrimp sound production patterns on Caribbean coral reefs: relationships with celestial cycles and environmental variables, Coral Reefs, vol.37, issue.2, pp.1-11, 2018.

T. H. Lin, S. H. Fang, and Y. Tsao, Improving biodiversity assessment via unsupervised separation of biological sounds from long-duration recordings, Scientific Reports, vol.7, issue.1, pp.1-10, 2017.

A. Lindseth and P. Lobel, Underwater Soundscape Monitoring and Fish, Bioacoustics: A Review. Fishes, vol.3, issue.3, p.36, 2018.

P. S. Lobel, Fish bioacoustics and behavior: passive acoustic detection and the application of a closed-circuit rebreather for field study, Marine Technology Society Journal, vol.35, pp.19-28, 2001.

P. S. Lobel, I. M. Kaatz, and A. N. Rice, Acoustical behavior of coral reef fishes. In Reproduction and sexuality in marine fishes, vol.307, 2010.

J. Lokrantz, M. Nyström, M. Thyresson, and C. Johansson, The non-linear relationship between body size and function in parrotfishes, Coral Reefs, vol.27, p.967, 2008.

J. Lossent, L. Di-iorio, C. A. Valentini-poirier, P. Boissery, and C. Gervaise, Mapping the diversity of spectral shapes discriminates between adjacent benthic biophonies, Marine Ecology Progress Series, vol.585, pp.31-48, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01714129

D. P. Loye and D. A. Proudfoot, Underwater noise due to marine life, The Journal of the Acoustical Society of America, vol.18, issue.2, pp.446-449, 1946.

E. Luckhurst and K. Luckhurst, Analysis of the Influence of Substrate Variables on Coral Reef Fish Communities, Marine Biology, vol.323, pp.317-323, 1978.

M. Lugli, Acoustics of fish shelters: Frequency response and gain properties, The Journal of the Acoustical Society of America, vol.132, issue.5, pp.3512-3524, 2012.

M. A. Macneil, N. A. Graham, J. E. Cinner, S. K. Wilson, I. D. Williams et al., Recovery potential of the world's coral reef fishes, 2015.

E. Maire, J. Cinner, L. Velez, C. Huchery, C. Mora et al., How accessible are coral reefs to people? A global assessment based on travel time, Ecology Letters, vol.19, issue.4, pp.351-360, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01925269

D. Mallet and D. Pelletier, Underwater video techniques for observing coastal marine biodiversity: A review of sixty years of publications, Fisheries Research, vol.154, pp.44-62, 2014.

D. Mallet, L. Wantiez, S. Lemouellic, L. Vigliola, and D. Pelletier, Complementarity of Rotating Video and Underwater Visual Census for Assessing Species Richness, Frequency and Density of Reef Fish on Coral Reef Slopes, PLoS One, vol.9, issue.1, 2014.

D. A. Mann and P. S. Lobel, Passive acoustic detection of sounds produced by the damselfish, Dascyllus albisella (Pomacentridae), Bioacoustics, vol.6, issue.3, pp.199-213, 1995.

D. A. Mann and T. M. Grothues, Short-term upwelling events modulate fish sound production at a mid-Atlantic Ocean observatory, Marine Ecology Progress Series, vol.375, pp.65-71, 2009.

T. R. Mcclanahan, N. A. Graham, M. A. Macneil, and J. E. Cinner, Biomass-based targets and the management of multispecies coral reef fisheries, Conservation Biology, vol.29, issue.2, pp.409-417, 2014.

T. R. Mcclanahan, N. A. Graham, M. A. Macneil, N. A. Muthiga, J. E. Cinner et al., Critical thresholds and tangible targets for ecosystem-based management of coral reef fisheries, Proceedings of the National Academy of Sciences, vol.108, issue.41, pp.17230-17233, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00852824

T. R. Mcclanahan, J. E. Cinner, C. Abunge, A. Rabearisoa, P. Mahatante et al., Perceived benefits of fisheries management restrictions in madagascar, Ecology and Society, vol.19, issue.1, 2014.

T. R. Mcclanahan, N. A. Graham, and E. S. Darling, Coral reefs in a crystal ball: Predicting the future from the vulnerability of corals and reef fishes to multiple stressors, Current Opinion in Environmental Sustainability, vol.7, pp.59-64, 2014.

J. N. Mcwilliam, R. D. Mccauley, C. Erbe, and M. J. Parsons, Patterns of biophonic periodicity on coral reefs in the Great Barrier Reef, Scientific Reports, vol.7, issue.1, pp.1-13, 2017.

J. N. Mcwilliam, R. D. Mccauley, C. Erbe, and M. J. Parsons, Soundscape diversity in the Great Barrier Reef : Lizard Island , a case study, Bioacoustics, vol.4622, pp.1-17, 2017.

J. N. Mcwilliam, Coral reef soundscapes: The use of passive acoustic monitoring for long-term ecological survey, 2018.

C. Mellin, L. Parrott, S. Andréfouët, C. J. Bradshaw, M. A. Macneil et al., Multi-scale marine biodiversity patterns inferred efficiently from habitat image processing, Ecological Applications, vol.22, pp.792-803, 2012.

C. Mellin, D. Mouillot, M. Kulbicki, T. R. Mcclanahan, L. Vigliola et al., Humans and seasonal climate variability threaten large-bodied coral reef fish with small ranges, Nature communications, vol.7, p.10491, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01282870

F. Moberg and C. Folke, Ecological goods and services of coral reef ecosystems, Ecological Economics, vol.29, issue.2, pp.215-233, 1999.

D. Mouillot, S. Villéger, V. Parravicini, M. Kulbicki, J. E. Arias-gonzález et al.,

D. R. Bellwood, Functional over-redundancy and high functional vulnerability in global fish faunas on tropical reefs, Proceedings of the National Academy of Sciences, vol.111, issue.38, pp.13757-13762, 2014.

P. J. Mumby, K. Broad, D. R. Brumbaugh, C. P. Dahlgren, A. R. Harborne et al., Coral reef habitats as surrogates of species, ecological functions, and ecosystem services, Conservation Biology, vol.22, issue.4, pp.941-951, 2008.

P. J. Mumby, Trends and frontiers for the science and management of the oceans, Current Biology, vol.27, issue.11, pp.431-434, 2017.

E. Myers, E. Harvey, B. Saunders, and M. Travers, Fine-scale patterns in the day, night and crepuscular composition of a temperate reef fish assemblage, Marine Ecology, vol.37, issue.3, pp.668-678, 2016.

S. L. Nedelec, S. D. Simpson, M. Holderied, A. N. Radford, G. Lecellier et al., Soundscapes and living communities in coral reefs: Temporal and spatial variation, Marine Ecology Progress Series, vol.524, pp.125-135, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01988764

J. Noda, C. Travieso, and D. Sánchez-rodríguez, Automatic taxonomic classification of fish based on their acoustic signals, Applied Sciences, vol.6, issue.12, p.443, 2016.

J. A. Nystuen, Rainfall measurements using underwater ambient noise, The Journal of the Acoustical Society of America, vol.79, issue.4, pp.972-982, 2005.

D. Obura, M. Gudka, F. A. Rabi, S. B. Gian, J. Bijoux et al., Coral Reef Status Report for the Western Indian Ocean, 2017.

D. Obura, W. Appeltans, N. Amornthammarong, G. Aeby, N. J. Bax et al., Coral Reef Monitoring, Reef Assessment Technologies, and Ecosystem-Based Management, Frontiers in Marine Science, vol.6, 2019.

C. Page, G. Coleman, R. Ninio, and K. Osborne, Long-term Monitoring of the Great Barrier Reef Standard Operational Procedure Number 7, Australian Institute of Marine Science, 2001.

E. Parmentier, J. P. Lagardère, P. Vandewalle, and M. L. Fine, Geographical variation in sound production in the anemonefish Amphiprion akallopisos, Proceedings of the Royal Society B: Biological Sciences, vol.272, pp.1697-1703, 1573.

E. Parmentier, X. Raick, D. Lecchini, K. Boyle, S. Wassenbergh et al., Unusual sound production mechanism in the triggerfish Rhinecanthus aculeatus (Balistidae), Journal of Experimental Biology, vol.220, issue.2, pp.186-193, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01472506

V. Parravicini, M. Kulbicki, D. R. Bellwood, A. M. Friedlander, J. E. Arias-gonzalez et al., Global patterns and predictors of tropical reef fish species richness, Ecography, vol.36, pp.1254-1262, 2013.

V. Parravicini, S. Villéger, T. R. Mcclanahan, J. E. Arias-gonzález, D. R. Bellwood et al., Global mismatch between species richness and vulnerability of reef fish assemblages, Ecology Letters, vol.17, pp.1101-1110, 2014.

C. T. Perry and L. Alvarez-filip, Changing geo-ecological functions of coral reefs in the Anthropocene, Functional Ecology, vol.33, pp.976-988, 2018.

Y. F. Phillips, M. Towsey, and P. Roe, Revealing the ecological content of long-duration audiorecordings of the environment through clustering and visualisation, PLoS ONE, vol.13, issue.3, pp.1-27, 2018.

J. J. Piercy, E. A. Codling, A. J. Hill, D. J. Smith, and S. D. Simpson, Habitat quality affects sound production and likely distance of detection on coral reefs, Marine Ecology Progress Series, vol.516, pp.35-47, 2014.

N. Pieretti, A. Farina, and D. Morri, A new methodology to infer the singing activity of an avian community: The Acoustic Complexity Index (ACI), Ecological Indicators, vol.11, issue.3, pp.868-873, 2011.

N. Pieretti, M. H. Duarte, R. S. Sousa-lima, M. Rodrigues, R. J. Young et al., Determining temporal sampling schemes for passive acoustic studies in different tropical ecosystems, Tropical Conservation Science, vol.8, issue.1, pp.215-234, 2015.

N. Pieretti, M. Martire, . Lo, A. Farina, and R. Danovaro, Marine soundscape as an additional biodiversity monitoring tool: A case study from the Adriatic Sea (Mediterranean Sea), Ecological Indicators, vol.83, pp.13-20, 2017.

B. C. Pijanowski, L. J. Villanueva-rivera, S. L. Dumyahn, A. Farina, B. L. Krause et al., Soundscape Ecology: The Science of Sound in the Landscape, BioScience, issue.3, pp.203-216, 2011.

B. C. Pijanowski, A. Farina, S. H. Gage, S. L. Dumyahn, and B. L. Krause, What is soundscape ecology? An introduction and overview of an emerging new science, Landscape Ecology, vol.26, issue.9, pp.1213-1232, 2011.

M. K. Pine, A. G. Jeffs, D. Wang, and C. A. Radford, The potential for vessel noise to mask biologically important sounds within ecologically significant embayments, Ocean & Coastal Management, vol.127, pp.63-73, 2016.

M. S. Pratchett, P. L. Munday, S. K. Wilson, N. A. Graham, J. E. Cinner et al., Effects of climate-induced coral bleaching on coral-reef fishes -Ecological and economic consequences, Oceanography and Marine Biology: An Annual Review, vol.46, pp.251-296, 2008.

F. Provost and T. Fawcett, Analysis and visualization of classifier performance: comparison under imprecise class and cost distributions, Proceedings of the Third International Conference on Knowledge Discovery and Data Mining, pp.43-48, 1997.

S. J. Purkis, A. C. Gleason, C. R. Purkis, A. C. Dempsey, P. G. Renaud et al., High-resolution habitat and bathymetry maps for 65,000 sq. km of Earth's remotest coral reefs, QGIS Geographic Information System. Open Source Geospatial Foundation Project, vol.38, issue.3, pp.467-488, 2018.

C. A. Radford, A. G. Jeffs, C. T. Tindle, R. G. Cole, and J. C. Montgomery, Bubbled waters: The noise generated by underwater breathing apparatus, Marine and Freshwater Behaviour and Physiology, vol.38, issue.4, pp.259-267, 2005.

C. A. Radford, A. G. Jeffs, C. T. Tindle, and J. C. Montgomery, Resonating sea urchin skeletons create coastal choruses, Marine Ecology Progress Series, vol.362, pp.37-43, 2008.

C. A. Radford, A. G. Jeffs, C. T. Tindle, and J. C. Montgomery, Temporal patterns in ambient noise of biological origin from a shallow water temperate reef, Oecologia, vol.156, issue.4, pp.921-929, 2008.

C. A. Radford, J. A. Stanley, C. T. Tindle, J. C. Montgomery, and A. G. Jeffs, Localised coastal habitats have distinct underwater sound signatures, Marine Ecology Progress Series, vol.401, pp.21-29, 2010.

C. A. Radford, J. A. Stanley, and A. G. Jeffs, Adjacent coral reef habitats produce different underwater sound signatures, Marine Ecology Progress Series, vol.505, pp.19-28, 2014.

G. H. Rau, E. L. Mcleod, and O. Hoegh-guldberg, The need for new ocean conservation strategies in a high-carbon dioxide world, Nature Climate Change, vol.2, issue.10, pp.720-724, 2012.

. R-core-team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2019.

J. P. Robinson, S. K. Wilson, S. Jennings, and N. A. Graham, Thermal stress induces persistently altered coral reef fish assemblages, Global Change Biology, vol.25, pp.2739-2750, 2019.

M. A. Roch, T. Scott-brandes, B. Patel, Y. Barkley, S. Baumann-pickering et al., Automated extraction of odontocete whistle contours, The Journal of the Acoustical Society of America, vol.130, issue.4, pp.2212-2223, 2011.

C. Roelfsema, E. Kovacs, J. C. Ortiz, N. H. Wolff, D. Callaghan et al., Coral reef habitat mapping: A combination of object-based image analysis and ecological modelling. Remote Sensing of Environment, vol.208, pp.27-41, 2018.

A. Rogers, J. L. Blanchard, and P. J. Mumby, Fisheries productivity under progressive coral reef degradation, Journal of applied ecology, vol.55, issue.3, pp.1041-1049, 2018.

T. Rossi, S. D. Connell, and I. Nagelkerken, The sounds of silence: Regime shifts impoverish marine soundscapes, Landscape Ecology, vol.32, pp.239-248, 2017.

P. Sale, Our dying planet: An ecologist's view of the crisis we face, 2011.

W. E. Schevill and B. Lawrence, A phonograph record of the underwater calls of delphinapterus leucus, 1950.

B. Schmitz and J. Herberholz, Snapping behaviour in intraspecific agonistic encounters in the snapping shrimp (Alpheus heterochaelis), Journal of Biosciences, vol.23, pp.623-632, 1998.

. Seagis, EventMeasure. SeaGIS Pty. Bacchus Marsh, 2008.

C. E. Shannon, Communication in the presence of noise, Proceedings of the institute of radio engineers, vol.37, pp.10-21, 1949.

C. E. Shannon and W. Weaver, The mathematical theory of communication, 1949.

S. D. Simpson, A. N. Radford, S. L. Nedelec, M. C. Ferrari, D. P. Chivers et al., Anthropogenic noise increases fish mortality by predation, Nature Communications, vol.7, pp.1-7, 2016.

E. M. Sogin, P. Anderson, P. Williams, C. S. Chen, and R. D. Gates, Application of 1H-NMR metabolomic profiling for reef-building corals, PLoS ONE, issue.10, p.9, 2014.

,

R. S. Sousa-lima, T. F. Norris, J. N. Oswald, and D. P. Fernandes, A review and inventory of fixed autonomous recorders for passive acoustic monitoring of marine mammals, Aquatic Mammals, vol.39, issue.1, pp.23-53, 2013.

M. Spalding, M. D. Spalding, C. Ravilious, and E. P. Green, World atlas of coral reefs, 2001.

D. S. Srivastava, Using local-regional richness plots to test for species saturation: pitfalls and potentials, Journal of Animal Ecology, vol.68, issue.1, pp.1-16, 1999.

E. Staaterman, A. N. Rice, D. A. Mann, and C. B. Paris, Soundscapes from a Tropical Eastern Pacific reef and a Caribbean Sea reef, Coral Reefs, vol.32, issue.2, pp.553-557, 2013.

E. Staaterman, C. B. Paris, H. A. Deferrari, D. A. Mann, A. N. Rice et al., Celestial patterns in marine soundscapes, Marine Ecology Progress Series, vol.508, pp.17-32, 2014.

E. Staaterman, M. B. Ogburn, A. H. Altieri, S. J. Brandl, J. Seemann et al., Bioacoustic measurements complement visual biodiversity surveys: preliminary evidence from four shallow marine habitats, Marine Ecology Progress Series, vol.575, pp.207-215, 2017.

C. D. Storlazzi, P. Dartnell, G. A. Hatcher, and A. E. Gibbs, End of the chain? Rugosity and finescale bathymetry from existing underwater digital imagery using structure-from-motion (SfM) technology, Coral Reefs, vol.35, issue.3, pp.889-894, 2016.

D. Stowell and M. D. Plumbley, Automatic large-scale classification of bird sounds is strongly improved by unsupervised feature learning, PeerJ, vol.2, 2014.

D. Stowell, M. D. Wood, H. Pamu?a, Y. Stylianou, and H. Glotin, Automatic acoustic detection of birds through deep learning: The first Bird Audio Detection challenge, Methods in Ecology and Evolution, vol.10, issue.3, pp.368-380, 2019.

J. Sueur, S. Pavoine, O. Hamerlynck, and S. Duvail, Rapid acoustic survey for biodiversity appraisal, PLoS ONE, issue.12, p.3, 2008.
URL : https://hal.archives-ouvertes.fr/ird-02149902

J. Sueur, T. Aubin, and C. Simonis, Equipment Review Seewave, a free modular tool for sound analysis and synthesis, Bioacoustics, vol.18, issue.2, pp.213-226, 2008.

J. Sueur, A. Farina, A. Gasc, N. Pieretti, and S. Pavoine, Acoustic indices for biodiversity assessment and landscape investigation, Acta Acustica United with Acustica, vol.100, issue.4, pp.772-781, 2014.

J. Sueur and A. Farina, Ecoacoustics: the Ecological Investigation and Interpretation of Environmental Sound, Biosemiotics, vol.8, issue.3, pp.493-502, 2015.

J. Sueur, Sound Analysis and Synthesis with R, 2018.

M. Towsey, L. Zhang, M. Cottman-fields, J. Wimmer, J. Zhang et al., Visualization of long-duration acoustic recordings of the environment, Procedia Computer Science, vol.29, pp.703-712, 2014.

M. Towsey, E. Znidersic, J. Broken-brow, K. Indraswari, D. M. Watson et al., Long-duration, false-colour spectrograms for detecting species in large audio data-sets, Journal of Ecoacoustics, vol.2, 2018.

T. C. Tricas and K. S. Boyle, Acoustic behaviors in Hawaiian coral reef fish communities, Marine Ecology Progress Series, vol.511, pp.1-16, 2014.

J. S. Ulloa, T. Aubin, D. Llusia, C. Bouveyron, and J. Sueur, Estimating animal acoustic diversity in tropical environments using unsupervised multiresolution analysis, Ecological Indicators, vol.90, pp.346-355, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01830049

J. S. Ulloa, A. Gasc, P. Gaucher, T. Aubin, M. Réjou-méchain et al., Screening large audio datasets to determine the time and space distribution of Screaming Piha birds in a tropical forest, Ecological Informatics, vol.31, pp.91-99, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01346004

W. Unep-wcmc, . Centre, . Wri, . Tnc-(-;-), and . Spalding, Global distribution of warm-water coral reefs, compiled from multiple sources including the Millennium Coral Reef Mapping Project. Version 1.3. Includes contributions from IMaRS-USF and IRD, UNEP World Conservation Monitoring Centre, 2001.

R. J. Urick, Principles of underwater sound 3rd edition, 1983.

R. Van-hooidonk, J. A. Maynard, D. Manzello, and S. Planes, Opposite latitudinal gradients in projected ocean acidification and bleaching impacts on coral reefs, Global Change Biology, vol.20, issue.1, pp.103-112, 2014.

R. Van-hooidonk, J. Maynard, J. Tamelander, J. Gove, G. Ahmadia et al., Local-scale projections of coral reef futures and implications of the Paris Agreement, Scientific Reports, vol.6, pp.1-8, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01441969

M. J. Van-oppen, J. K. Oliver, H. M. Putnam, and R. D. Gates, Building coral reef resilience through assisted evolution, Proceedings of the National Academy of Sciences of the United States of America, vol.112, pp.2307-2313, 2015.

A. Vergés, P. D. Steinberg, M. E. Hay, A. G. Poore, A. H. Campbell et al., The tropicalization of temperate marine ecosystems: Climate-mediated changes in herbivory and community phase shifts, Proceedings of the Royal Society B: Biological Sciences, p.281, 1789.

J. E. Veron, Corals of the World Vols 1-3. Australian Institute of Marine Science, 2000.

M. Versluis, B. Schmitz, A. Von-der-heydt, and D. Lohse, How Snapping Shrimp Snap: Through Cavitating Bubbles, Science, vol.289, issue.5487, pp.2114-2117, 2000.

L. J. Villanueva-rivera and B. C. Pijanowski, soundecology: soundscape ecology, 2016.

S. Villon, D. Mouillot, M. Chaumont, E. S. Darling, G. Subsol et al., A Deep Learning algorithm for accurate and fast identification of coral reef fishes in underwater videos, PeerJ Preprints, vol.6, 2018.

C. C. Wall, P. Simard, M. Lindemuth, C. Lembke, D. F. Naar et al., Temporal and spatial mapping of red grouper Epinephelus morio sound production, Journal of fish biology, vol.85, issue.5, pp.1470-1488, 2014.

J. Wang, B. Liu, G. Kan, G. Li, and X. Meng, Laboratory measurements of sound speed and attenuation dispersion in calcareous sediments from coral reefs, The Journal of the Acoustical Society of America, vol.142, issue.4, pp.2623-2623, 2017.

M. Watanabe, M. Sekine, E. Hamada, M. Ukita, and T. Imai, Monitoring of shallow sea environment by using snapping shrimps. Water science and technology, vol.46, pp.419-424, 2002.

S. C. Webb, Broadband seismology and noise under the ocean, Reviews of Geophysics, vol.36, pp.105-142, 1998.

L. M. Wedding, S. Jorgensen, C. A. Lepczyk, and A. M. Friedlander, Remote sensing of threedimensional coral reef structure enhances predictive modeling of fish assemblages. Remote Sensing in Ecology and Conservation, 2019.

G. M. Wenz, Review of underwater acoustics research: noise. The Journal of the, vol.51, pp.1010-1024, 1972.

C. Wild, O. Hoegh-guldberg, M. S. Naumann, M. F. Colombo-pallotta, M. Ateweberhan et al.,

Y. Loya, Climate change impedes scleractinian corals as primary reef ecosystem engineers. Marine and Freshwater research, vol.62, pp.205-215, 2011.

G. J. Williams and N. A. Graham, Rethinking coral reef functional futures, Functional Ecology, vol.33, issue.6, pp.942-947, 2019.

G. J. Williams, N. A. Graham, J. B. Jouffray, A. V. Norström, M. Nyström et al., Coral reef ecology in the Anthropocene, Functional Ecology, vol.33, pp.1014-1022, 2019.

S. K. Wilson, S. C. Burgess, A. J. Cheal, M. Emslie, R. Fisher et al., Habitat utilization by coral reef fish: implications for specialists vs. generalists in a changing environment, Journal of Animal Ecology, vol.77, issue.2, pp.220-228, 2008.

A. J. Woodhead, C. C. Hicks, A. V. Norström, G. J. Williams, and N. A. Graham, Coral reef ecosystem services in the Anthropocene, Functional Ecology, vol.33, pp.1023-1034, 2019.

R. Zelick, D. A. Mann, and A. N. Popper, Acoustic communication in fishes and frogs, Comparative hearing: fish and amphibians, pp.363-411, 1999.