C. H. Ainsworth, B. Ferriss, E. Leblond, and S. Guénette, The Bay of Biscay, France: 1998 and 1970 models. Fisheries impacts on North Atlantic ecosystems: models and analyses, 2001.

M. Alcaraz, E. Saiz, A. Calbet, I. Trepat, and E. Broglio, Estimating zooplankton biomass through image analysis, Marine Biology, vol.143, pp.305-315, 2003.

K. R. Allen, Relation Between Production and Biomass, Journal of the Fisheries Research Board of Canada, vol.28, issue.10, pp.1573-1581, 1971.
DOI : 10.1139/f71-236

J. M. Arcos, Foraging ecology of seabirds at sea: significance of commercial fisheries in the NW Mediterranean, Animal Biology Department, 2001.

F. Baeta, M. J. Costa, and H. Cabral, Trammel nets??? ghost fishing off the Portuguese central coast, Fisheries Research, vol.98, issue.1-3, pp.33-39, 2009.
DOI : 10.1016/j.fishres.2009.03.009

A. Bode, M. T. Alvarez-ossorio, P. Carrera, and J. Lorenzo, Reconstruction of trophic pathways between plankton and the North Iberian sardine (<i>Sardina pilchardus</i>) using stable isotopes, Scientia Marina, vol.68, issue.1, pp.165-178, 2004.
DOI : 10.3989/scimar.2004.68n1165

I. A. Boyd, Energetics: consequences for fitness Marine mammal biology -an evolutionary approach, Blackwell Science, pp.247-278, 2002.

S. Plateau, New Zealand: a low biomass, high transfer efficiency system, Journal of Experimental Marine Biology and Ecology, vol.289, pp.223-262

T. Brey, C. Müller-wiegmann, Z. M. Zittier, and W. Hagen, Body composition in aquatic organisms ??? A global data bank of relationships between mass, elemental composition and energy content, Journal of Sea Research, vol.64, issue.3, pp.334-340, 2010.
DOI : 10.1016/j.seares.2010.05.002

H. I. Browman, P. Cury, R. Hilborn, S. Jennings, H. K. Lotze et al., Perspectives on ecosystem-based approaches to the management of marine resources, Marine Ecology Progress Series, vol.274, pp.269-303, 2004.
DOI : 10.3354/meps274269

C. Byron, J. Link, B. Costa-pierce, and D. Bengtson, Modeling ecological carrying capacity of shellfish aquaculture in highly flushed temperate lagoons, Aquaculture, vol.314, issue.1-4, pp.87-99, 2011.
DOI : 10.1016/j.aquaculture.2011.02.019

H. N. Cabral and A. G. Murta, The diet of blue whiting, hake, horse mackerel and mackerel off Portugal, Journal of Applied Ichthyology, vol.5, issue.1, pp.14-23, 2002.
DOI : 10.1016/S0165-7836(98)00111-8

G. Certain and V. Bretagnolle, Monitoring seabirds population in marine ecosystem: The use of strip-transect aerial surveys, Remote Sensing of Environment, vol.112, issue.8, pp.3314-3322, 2008.
DOI : 10.1016/j.rse.2008.01.019
URL : https://hal.archives-ouvertes.fr/hal-00323809

G. Certain, J. Masse, O. Van-canneyt, P. Petitgas, G. Doremus et al., Investigating the coupling between small pelagic fish and marine top predators using data collected from ecosystem-based surveys, Marine Ecology Progress Series, vol.422, pp.23-39, 2011.
DOI : 10.3354/meps08932

G. Certain, V. Ridoux, O. Van-canneyt, and V. Bretagnolle, Delphinid spatial distribution and abundance estimates over the shelf of the Bay of Biscay, ICES Journal of Marine Science, vol.65, issue.4, pp.656-666, 2008.
DOI : 10.1093/icesjms/fsn046
URL : https://hal.archives-ouvertes.fr/hal-00323744

V. Christensen, Ecosystem maturity ??? towards quantification, Ecological Modelling, vol.77, issue.1, pp.3-32, 1995.
DOI : 10.1016/0304-3800(93)E0073-C

V. Christensen and D. Pauly, ECOPATH II ??? a software for balancing steady-state ecosystem models and calculating network characteristics, Ecological Modelling, vol.61, issue.3-4, pp.169-185, 1992.
DOI : 10.1016/0304-3800(92)90016-8

V. Christensen and D. Pauly, Trophic models of aquatic ecosystems. International Center for Living Aquatic Resources Management; The International Council for the Exploration of the Sea; The Danish International Development Agency, 1993.

V. Christensen and C. J. Walters, Ecopath with Ecosim: methods, capabilities and limitations, Ecological Modelling, vol.172, issue.2-4, pp.109-139, 2004.
DOI : 10.1016/j.ecolmodel.2003.09.003

V. Christensen, C. J. Walters, R. Ahrens, J. Alder, J. Buszowski et al., Database-driven models of the world's Large Marine Ecosystems, Ecological Modelling, vol.220, issue.17, 1984.
DOI : 10.1016/j.ecolmodel.2009.04.041

M. Coll, S. Libralato, S. Tudela, I. Palomera, and F. Pranovi, Ecosystem Overfishing in the Ocean, PLoS ONE, vol.190, issue.12, p.3881, 2008.
DOI : 10.1371/journal.pone.0003881.s007

M. Coll, A. Santojanni, I. Palomera, S. Tudela, and E. Arneri, An ecological model of the Northern and Central Adriatic Sea: Analysis of ecosystem structure and fishing impacts, Journal of Marine Systems, vol.67, issue.1-2, pp.119-154, 2007.
DOI : 10.1016/j.jmarsys.2006.10.002

M. Coll, L. J. Shannon, C. L. Moloney, I. Palomera, and S. Tudela, Comparing trophic flows and fishing impacts of a NW Mediterranean ecosystem with coastal upwelling systems by means of standardized models and indicators, Ecological Modelling, vol.198, issue.1-2, pp.53-70, 2006.
DOI : 10.1016/j.ecolmodel.2006.04.009

P. Cury, A. Bakun, R. J. Crawford, A. Jarre, R. A. Quinones et al., Small pelagics in upwelling systems: patterns of interaction and structural changes in ???wasp-waist??? ecosystems, ICES Journal of Marine Science, vol.57, issue.3, pp.603-618, 2000.
DOI : 10.1006/jmsc.2000.0712

P. Cury, L. J. Shannon, and Y. J. Shin, The functioning of marine ecosystems: a fisheries perspective Responsible fisheries in the marine ecosystem, pp.103-125, 2003.

P. M. Cury, L. J. Shannon, J. P. Roux, G. M. Daskalov, A. Jarre et al., Trophodynamic indicators for an ecosystem approach to fisheries, ICES Journal of Marine Science, vol.62, issue.3, pp.430-442, 2005.
DOI : 10.1016/j.icesjms.2004.12.006

G. M. Daskalov, A. N. Grishin, S. Rodionov, and V. Mihneva, Trophic cascades triggered by overfishing reveal possible mechanisms of ecosystem regime shifts, Proceedings of the National Academy of Sciences, vol.104, issue.25, pp.10518-10523, 2007.
DOI : 10.1073/pnas.0701100104

P. Diaz, J. Santos, F. Velasco, A. Serrano, and N. Perez, Anglerfish discard estimates and patterns in Spanish Northeast Atlantic trawl fisheries, ICES Journal of Marine Science, vol.65, issue.7, pp.1350-1361, 2008.
DOI : 10.1093/icesjms/fsn127

K. T. Frank, B. Petrie, and N. L. Shackell, The ups and downs of trophic control in continental shelf ecosystems, Trends in Ecology & Evolution, vol.22, issue.5, pp.236-242, 2007.
DOI : 10.1016/j.tree.2007.03.002

E. A. Fulton, A. D. Smith, and C. R. Johnson, Effect of complexity on marine ecosystem models, Marine Ecology Progress Series, vol.253, pp.1-16, 2003.
DOI : 10.3354/meps253001

J. A. Furhman and F. Azam, Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters: Evaluation and field results, Marine Biology, vol.33, issue.2, pp.109-120, 1982.
DOI : 10.1007/BF00397184

K. J. Gaston, Global patterns in biodiversity, Nature, vol.405, issue.6783, pp.220-227, 2000.
DOI : 10.1038/35012228

D. Grémillet, L. Pichegru, G. Kuntz, A. G. Woakes, S. Wilkinson et al., A junk-food hypothesis for gannets feeding on fishery waste, Proceedings of the Royal Society B: Biological Sciences, vol.33, issue.2, pp.1149-1156, 2008.
DOI : 10.1093/icesjms/fsl022

J. Hall-spencer, V. Allain, and J. H. Fossa, Trawling damage to Northeast Atlantic ancient coral reefs, Proceedings of the Royal Society B: Biological Sciences, vol.269, issue.1490, pp.507-511, 2002.
DOI : 10.1098/rspb.2001.1910

S. J. Hall, The effects of fishing on marine ecosystems and communities, 1999.

M. R. Heithaus, A. Frid, A. J. Wirsing, and B. Worm, Predicting ecological consequences of marine top predator declines, Trends in Ecology & Evolution, vol.23, issue.4, pp.202-210, 2008.
DOI : 10.1016/j.tree.2008.01.003

R. Herendeen, Energy intensity, residence time, exergy, and ascendency in dynamic ecosystems, Ecological Modelling, vol.48, issue.1-2, pp.19-44, 1989.
DOI : 10.1016/0304-3800(89)90058-6

J. J. Heymans and D. Baird, A carbon flow model and network analysis of the northern Benguela upwelling system, Namibia, Ecological Modelling, vol.126, issue.1, pp.9-32, 2000.
DOI : 10.1016/S0304-3800(99)00192-1

J. M. Hoenig, Empirical use of longevity data to estimate mortality rates, Fishery Bulletin, vol.82, pp.898-903, 1983.

G. L. Hunt, G. S. Drew, J. Jahncke, and J. F. Piatt, Prey consumption and energy transfer by marine birds in the Gulf of Alaska, Deep Sea Research Part II: Topical Studies in Oceanography, vol.52, issue.5-6, pp.781-797, 2005.
DOI : 10.1016/j.dsr2.2004.12.024

J. G. Hunt and S. Mckinnell, Interplay between top-down, bottom-up, and wasp-waist control in marine ecosystems, Progress in Oceanography, vol.68, issue.2-4, pp.115-124, 2006.
DOI : 10.1016/j.pocean.2006.02.008

J. M. Huthnance, J. T. Holt, and S. L. Wakelin, Deep ocean exchange with west-European shelf seas, Ocean Science, vol.5, issue.4, pp.621-634, 2009.
DOI : 10.5194/os-5-621-2009

X. Irigoien, J. A. Fernandes, P. Grosjean, K. Denis, A. Albaina et al., Spring zooplankton distribution in the Bay of Biscay from 1998 to 2006 in relation with anchovy recruitment, Journal of Plankton Research, vol.31, issue.1, pp.1-17, 2009.
DOI : 10.1093/plankt/fbn096

G. D. Jackson and R. K. O-'dor, Time, space and the ecophysiology of squid growth, life in the fast lane, Vie et Milieu, vol.51, pp.205-215, 2001.

J. L. Jimeno, A mass balance model of the Bay of Biscay ecosystem. Master Thesis, AZTI-Tecnalia, Marine research division, area of pelagic resources management, 2010.

S. E. Jorgensen, S. N. Nielsen, and L. A. Jorgensen, Handbook of ecological parameters and ecotoxicology, 1991.

C. Labry, A. Herbland, and D. Delmas, The role of phosphorus on planktonic production of the Gironde plume waters in the Bay of Biscay, Journal of Plankton Research, vol.24, issue.2, pp.97-117, 2002.
DOI : 10.1093/plankt/24.2.97

M. R. Landry and R. P. Hassett, Estimating the grazing impact of marine micro-zooplankton, Marine Biology, vol.26, issue.3, pp.283-288, 1982.
DOI : 10.1007/BF00397668

L. Loc-'h and F. , Structure, fonctionnement, évolution des communautés benthiques des fonds meubles exploités du plateau continental Nord-Gascogne, Thèse de Doctorat, 2004.

L. Loc-'h, F. Hily, C. Grall, and J. , Benthic community and food web structure on the continental shelf of the Bay of Biscay (North Eastern Atlantic) revealed by stable isotopes analysis, Journal of Marine Systems, vol.72, pp.17-34, 2008.

R. Leaper and D. Lavigne, How much do large whales eat, Journal of Cetacean Research and Management, vol.9, pp.179-188, 2007.

J. P. Léauté, European Union fishing fleet in the Bay of Biscay, seen from the sky, 1998.

S. Libralato, V. Christensen, and D. Pauly, A method for identifying keystone species in food web models, Ecological Modelling, vol.195, issue.3-4, pp.153-171, 2006.
DOI : 10.1016/j.ecolmodel.2005.11.029

S. Libralato, M. Coll, S. Tudela, I. Palomera, and F. Pranovi, Novel index for quantification of ecosystem effects of fishing as removal of secondary production, Marine Ecology Progress Series, vol.355, pp.107-129, 2008.
DOI : 10.3354/meps07224

J. S. Link, Adding rigor to ecological network models by evaluating a set of pre-balance diagnostics: A plea for PREBAL, Ecological Modelling, vol.221, issue.12, pp.1580-1591, 2010.
DOI : 10.1016/j.ecolmodel.2010.03.012

P. Lorance, J. A. Bertrand, A. Brind-'amour, M. J. Rochet, and V. M. Trenkel, Assessment of impacts from human activities on ecosystem components in the Bay of Biscay in the early 1990s, Aquatic Living Resources, vol.22, issue.4, pp.409-431, 2009.
DOI : 10.1051/alr/2009049

E. Marquis, N. Niquil, and C. Dupuy, in press. Does the study of microzooplankton community size structure effectively define their dynamics? Investigation in the Bay, Biscay

L. Meynier, C. Pusineri, J. Spitz, M. B. Santos, G. J. Pierce et al., Intraspecific dietary variation in the short-beaked common dolphin (Delphinus delphis) in the Bay of, 2008.

M. E. Monaco and R. E. Ulanowicz, Comparative ecosystem trophic structure of three U.S. mid-Atlantic estuaries, Marine Ecology Progress Series, vol.161, pp.239-254, 1997.
DOI : 10.3354/meps161239

J. C. Moore, E. L. Berlow, D. C. Coleman, P. C. De-ruiter, Q. Dong et al., Detritus, trophic dynamics and biodiversity, Ecology Letters, vol.69, issue.7, pp.584-600, 2004.
DOI : 10.1111/j.1461-0248.2004.00606.x

B. Nelson, Seabirds: their biology and ecology, 1979.

S. G. Nilsson and I. N. Nilsson, Numbers, Food Consumption, and Fish Predation by Birds in Lake Mockeln, Southern Sweden, Ornis Scandinavica, vol.7, issue.1, pp.61-70, 1976.
DOI : 10.2307/3676175

E. P. Odum, The Strategy of Ecosystem Development, Science, vol.164, issue.3877, pp.262-270, 1969.
DOI : 10.1126/science.164.3877.262

R. T. Paine, Food Web Complexity and Species Diversity, The American Naturalist, vol.100, issue.910, pp.65-75, 1966.
DOI : 10.1086/282400

M. L. Palomares and D. Pauly, Predicting food consumption of fish populations as functions of mortality, food type, morphometrics, temperature and salinity, Marine and Freshwater Research, vol.49, issue.5, pp.447-453, 1998.
DOI : 10.1071/MF98015

D. Pauly, On the interrelationships between natural mortality, growth parameters, and mean environmental temperature in 175 fish stocks, Journal du Conseil Permanent International pour l'Exploration de la Mer, pp.175-192, 1980.
DOI : 10.1093/icesjms/39.2.175

D. Pauly and V. Christensen, Primary production required to sustain global fisheries, Nature, vol.374, issue.6519, pp.255-257, 1995.
DOI : 10.1038/374255a0

E. E. Plagànyi, Models for an ecosystem approach to fisheries. FAO Fisheries Technical Paper, 2007.

E. E. Plagànyi and D. S. Butterworth, A critical look at the potential of Ecopath with ecosim to assist in practical fisheries management, African Journal of Marine Science, vol.26, issue.1, pp.261-287, 2004.
DOI : 10.2989/18142320409504061

B. Planque, P. Lazure, and A. M. Jégou, Detecting hydrological landscapes over the Bay of Biscay continental shelf in spring, Climate Research, vol.28, pp.41-52, 2004.
DOI : 10.3354/cr028041

T. Platt and B. Irwin, Caloric content of phytoplankton, Limnology and Oceanography, vol.18, issue.2, pp.306-309, 1973.
DOI : 10.4319/lo.1973.18.2.0306

J. J. Polovina, Model of a coral reef ecosystem, Coral Reefs, vol.290, issue.1, pp.1-11, 1984.
DOI : 10.1007/BF00306135

K. G. Porter and Y. S. Feig, The use of DAPI for identifying and counting aquatic microflora1, Limnology and Oceanography, vol.25, issue.5, pp.943-948, 1980.
DOI : 10.4319/lo.1980.25.5.0943

F. Pranovi and J. S. Link, Ecosystem exploitation and trophodynamic indicators: A comparison between the Northern Adriatic Sea and Southern New England, Progress in Oceanography, vol.81, issue.1-4, pp.149-164, 2009.
DOI : 10.1016/j.pocean.2009.04.008

M. J. Rochet and V. Trenkel, Which community indicators can measure the impact of fishing? A review and proposals, Canadian Journal of Fisheries and Aquatic Sciences, vol.60, issue.1, pp.86-99, 2003.
DOI : 10.1139/f02-164

F. Sanchez and I. Olaso, Effects of fisheries on the Cantabrian Sea shelf ecosystem, Ecological Modelling, vol.172, issue.2-4, pp.151-174, 2004.
DOI : 10.1016/j.ecolmodel.2003.09.005

P. Schwinghamer, B. Hargrave, D. Peer, and C. M. Hawkins, Partitioning of production and respiration among size groups of organisms in an intertidal benthic community, Marine Ecology Progress Series, vol.31, pp.131-142, 1986.
DOI : 10.3354/meps031131

L. J. Shannon, M. Coll, S. Neira, P. M. Cury, and J. P. Roux, Impacts of fishing and climate change explored using trophic models Climate change and small pelagic fish, pp.158-190, 2009.

J. Spitz, E. Mourocq, V. Schoen, and V. Ridoux, Proximate composition and energy content of forage species from the Bay of Biscay: high- or low-quality food?, ICES Journal of Marine Science, vol.67, issue.5, pp.909-915, 2010.
DOI : 10.1093/icesjms/fsq008

J. Spitz, E. Richard, L. Meynier, C. Pusineri, and V. Ridoux, Dietary plasticity of the oceanic striped dolphin, Stenella coeruleoalba, in the neritic waters of the Bay of Biscay, Journal of Sea Research, vol.55, issue.4, pp.309-320, 2006.
DOI : 10.1016/j.seares.2006.02.001

J. Spitz, Y. Rousseau, and V. Ridoux, Diet overlap between harbour porpoise and bottlenose dolphin: An argument in favour of interference competition for food?, Estuarine, Coastal and Shelf Science, vol.70, issue.1-2, pp.259-270, 2006.
DOI : 10.1016/j.ecss.2006.04.020
URL : https://hal.archives-ouvertes.fr/hal-00150198

J. H. Steele, The structure of marine ecosystems, 1974.
DOI : 10.4159/harvard.9780674592513

E. Steeman-nielsen, The Use of Radio-active Carbon (C14) for Measuring Organic Production in the Sea, ICES Journal of Marine Science, vol.18, issue.2, pp.117-140, 1952.
DOI : 10.1093/icesjms/18.2.117

N. C. Stenseth, M. Llope, R. Anadón, L. Ciannelli, K. S. Chan et al., Seasonal plankton dynamics along a cross-shelf gradient, Proceedings of the Royal Society B: Biological Sciences, vol.84, issue.6744, pp.2831-2838, 2006.
DOI : 10.1038/22941

H. Tallis, P. S. Levin, M. Ruckelshaus, S. E. Lester, K. L. Mcleod et al., The many faces of ecosystem-based management: Making the process work today in real places, Marine Policy, vol.34, issue.2, pp.340-348, 2010.
DOI : 10.1016/j.marpol.2009.08.003

V. M. Trenkel and H. J. Skaug, Disentangling the effects of capture efficiency and population abundance on catch data using random effects models, ICES Journal of Marine Science, vol.62, issue.8, pp.1543-1555, 2005.
DOI : 10.1016/j.icesjms.2005.05.010

A. W. Trites, P. A. Livingston, M. C. Vasconcellos, S. Mackinson, A. M. Springer et al., Ecosystem change and the decline of marine mammals in the Eastern Bering Sea: testing the ecosystem shift and commercial whaling hypotheses, Fisheries Centre Research Reports, vol.7, issue.1, 1999.

A. W. Trites and D. Pauly, Estimating mean body masses of marine mammals from maximum body lengths, Canadian Journal of Zoology, vol.76, issue.5, pp.886-896, 1998.
DOI : 10.1139/z97-252

S. Tudela, M. Coll, and I. Palomera, Developing an operational reference framework for fisheries management on the basis of a two-dimensional index of ecosystem impact, ICES Journal of Marine Science, vol.62, issue.3, pp.585-591, 2005.
DOI : 10.1016/j.icesjms.2005.01.008

R. E. Ulanowicz, Growth and development: ecosystem phenomenology, 1986.
DOI : 10.1007/978-1-4612-4916-0

R. E. Ulanowicz and C. J. Puccia, Mixed trophic impacts in ecosystems, Coenoses, vol.5, pp.7-16, 1990.

M. Varela, Phytoplankton ecology in the Bay of Biscay, Scientia Marina, vol.60, pp.45-53, 1996.

A. F. Vézina and T. Platt, Food web dynamics in the ocean. I. Best-estimates of flow networks using inverse methods, Marine Ecology Progress Series, vol.42, pp.269-287, 1988.
DOI : 10.3354/meps042269

D. M. Ware and R. E. Thomson, Bottom-Up Ecosystem Trophic Dynamics Determine Fish Production in the Northeast Pacific, Science, vol.308, issue.5726, 2005.
DOI : 10.1126/science.1109049

J. P. Whitehead, FAO species catalogue -Clupeoid fishes of the world (suborder: clupeoidei) -An annoted and illustrated catalogue of the herrings, sardines, pilchards, sprats, shads, anchovies and wolf-herrings, p.53, 1985.

F. Wulff and R. E. Ulanowicz, A comparative anatomy of the Baltic Sea and Chesapeake ecosystems Network analysis in marine ecology -methods and applications, pp.232-256, 1989.

C. S. Yentsch and D. W. Menzel, A method for the determination of phytoplankton chlorophyll and phaeophytin by fluorescence, Deep Sea Research and Oceanographic Abstracts, vol.10, issue.3, pp.221-231, 1963.
DOI : 10.1016/0011-7471(63)90358-9