J. M. Olesen, F. J. Van-veen, P. H. Warren, and G. Woodward, Ecological networks ? beyond food webs, J Anim Ecol, vol.78, pp.253-269, 2009.

K. Jax, Function and ???functioning??? in ecology: what does it mean?, Oikos, vol.96, issue.3, pp.641-648, 2005.
DOI : 10.1007/978-3-642-58001-7_13

M. Kearney and W. Porter, Mechanistic niche modelling: combining physiological and spatial data to predict species??? ranges, Ecology Letters, vol.36, issue.4, pp.334-350, 2009.
DOI : 10.1093/icb/19.1.331

R. Kirby and C. Retière, Comparing environmental effects of Rance and Severn barrages, Proceedings of the Institution of Civil Engineers - Maritime Engineering, vol.162, issue.1, pp.11-26, 2009.
DOI : 10.1680/maen.2009.162.1.11

C. Klok, Model instruments for marine biodiversity policy. A quick scan. Statutory Research Tasks Unit for, Nature & the Environment, 2009.

L. Goff, C. Lavaud, R. Cugier, P. Jean, F. Flye-sainte-marie et al., A coupled biophysical model for the distribution of the great scallop Pecten maximus in the English Channel, Journal of Marine Systems, vol.167, pp.55-67, 2017.
DOI : 10.1016/j.jmarsys.2016.10.013

URL : https://hal.archives-ouvertes.fr/hal-01394278

D. Leguerrier, N. Niquil, N. Boileau, J. Rzeznik, P. Sauriau et al., Numerical analysis of the food web of an intertidal mudflat ecosystem on the Atlantic coast of France, Marine Ecology Progress Series, vol.246, pp.17-37, 2003.
DOI : 10.3354/meps246017

M. A. Leibold, The Niche Concept Revisited: Mechanistic Models and Community Context, Ecology, vol.76, issue.5, pp.1371-1382, 1995.
DOI : 10.2307/1938141

M. A. Leibold and M. A. Mcpeek, COEXISTENCE OF THE NICHE AND NEUTRAL PERSPECTIVES IN COMMUNITY ECOLOGY, Ecology, vol.87, issue.6, pp.1399-1410, 2006.
DOI : 10.1038/nature03211

R. Levins, Evolution in changing environments: some theoretical explorations, 1968.

B. T. Martin, E. I. Zimmer, V. Grimm, and T. Jager, Dynamic Energy Budget theory meets individual-based modelling: a generic and accessible implementation, Methods in Ecology and Evolution, vol.56, issue.2, pp.445-449, 2012.
DOI : 10.1016/j.seares.2006.03.001

URL : http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00168.x/pdf

M. P. Marzloff, J. M. Dambacher, C. R. Johnson, L. R. Little, and S. D. Frusher, Exploring alternative states in ecological systems with a qualitative analysis of community feedback, Ecological Modelling, vol.222, issue.15, pp.2651-2662, 2011.
DOI : 10.1016/j.ecolmodel.2011.03.040

B. J. Mcgill, B. J. Enquist, E. Weiher, and M. Westoby, Rebuilding community ecology from functional traits, Trends in Ecology & Evolution, vol.21, issue.4, pp.178-185, 2006.
DOI : 10.1016/j.tree.2006.02.002

B. J. Mcgill, R. S. Etienne, J. S. Gray, D. Alonso, M. J. Anderson et al., Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework, Ecology Letters, vol.42, issue.10, pp.995-1015, 2007.
DOI : 10.1098/rstb.1925.0002

P. S. Meadows, A. Meadows, and J. M. Murray, Biological modifiers of marine benthic seascapes: Their role as ecosystem engineers, Geomorphology, vol.157, issue.158, pp.31-48, 2012.
DOI : 10.1016/j.geomorph.2011.07.007

M. Ortiz and M. Wolff, Application of loop analysis to benthic systems in northern Chile for the elaboration of sustainable management strategies, Marine Ecology Progress Series, vol.242, pp.15-27, 2002.
DOI : 10.3354/meps242015

M. Ortiz and M. Wolff, Dynamical simulation of mass-balance trophic models for benthic communities of north-central Chile: assessment of resilience time under alternative management scenarios, Ecological Modelling, vol.148, issue.3, pp.277-291, 2002.
DOI : 10.1016/S0304-3800(01)00454-9

M. Ortiz and M. Wolff, Trophic models of four benthic communities in Tongoy Bay (Chile): comparative analysis and preliminary assessment of management strategies, Journal of Experimental Marine Biology and Ecology, vol.268, issue.2, pp.205-235, 2002.
DOI : 10.1016/S0022-0981(01)00385-9

D. Pauly, V. Christensen, and C. Walters, Ecopath, Ecosim, and Ecospace as tools for evaluating ecosystem impact of fisheries, ICES Journal of Marine Science, vol.57, issue.3, pp.697-706, 2000.
DOI : 10.1006/jmsc.2000.0726

T. H. Pearson, Functional group ecology in soft-sediment marine benthos: The role of bioturbation, Oceanogr Mar Biol, vol.39, pp.233-267, 2001.

O. L. Petchey, A. P. Beckerman, J. O. Riede, and P. H. Warren, Size, foraging, and food web structure, Proceedings of the National Academy of Sciences, vol.86, issue.1, pp.4191-4196, 2008.
DOI : 10.1890/05-0379

URL : http://www.pnas.org/content/105/11/4191.full.pdf

J. Pineda, N. B. Reyns, and V. R. Starczak, Complexity and simplification in understanding recruitment in benthic populations, Population Ecology, vol.30, issue.1, pp.17-32, 2009.
DOI : 10.4319/lo.2006.51.5.1982

C. J. Puccia and R. Levins, Qualitative modeling of complex systems, 1985.
DOI : 10.4159/harvard.9780674435070

H. Reiss, S. Cunze, K. König, H. Neumann, and I. Kröncke, Species distribution modelling of marine benthos: a??North Sea case study, Marine Ecology Progress Series, vol.442, pp.71-86, 2011.
DOI : 10.3354/meps09391

C. Retière, Contribution à la connaissance des peuplements benthiques du golfe Normano-Breton, 1979.

C. Rigolet, S. F. Dubois, and E. Thiébaut, Benthic control freaks: Effects of the tubiculous amphipod Haploops nirae on the specific diversity and functional structure of benthic communities, Journal of Sea Research, vol.85, pp.413-427, 2014.
DOI : 10.1016/j.seares.2013.07.013

URL : https://hal.archives-ouvertes.fr/hal-01140607

J. Roughgarden, Y. Iwasa, and C. Baxter, Demographic Theory for an Open Marine Population with Space-Limited Recruitment, Ecology, vol.66, issue.1, pp.54-67, 1985.
DOI : 10.2307/1941306

M. Savina and A. Ménesguen, The growth of the banded carpet shell (Paphia rhombo??des) in a contrasted region, the English Channel (Western Europe): A modelling study, Ecological Modelling, vol.205, issue.1-2, pp.39-51, 2007.
DOI : 10.1016/j.ecolmodel.2007.01.014

C. Scherer, F. Jeltsch, V. Grimm, and N. Blaum, Merging trait-based and individual-based modelling: An animal functional type approach to explore the responses of birds to climatic and land use changes in semi-arid African savannas, Ecological Modelling, vol.326, pp.75-89, 2016.
DOI : 10.1016/j.ecolmodel.2015.07.005

Y. Shin and P. Cury, Interactions trophiques fond????es sur la taille et dynamiques des communaut????s de poissons marins : exploration ???? l'aide d'un mod????le spatial individus-centr????., Aquatic Living Resources, vol.14, issue.2, pp.65-80, 2001.
DOI : 10.1016/S0990-7440(01)01106-8

P. Snelgrove and C. Butman, Animal-sediment relationships revisited: cause versus effect, Oceanogr Mar Biol, vol.32, pp.111-177, 1994.

W. J. Sutherland, R. P. Freckleton, H. C. Godfray, S. R. Beissinger, T. Benton et al., Identification of 100 fundamental ecological questions, Journal of Ecology, vol.3, issue.3, pp.58-67, 2013.
DOI : 10.1111/j.2041-210X.2011.00164.x

URL : http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12025/pdf

J. R. Svensson and D. J. Marshall, Limiting resources in sessile systems: food enhances diversity and growth of suspension feeders despite available space, Ecology, vol.96, issue.3, pp.819-827, 2015.
DOI : 10.1006/jmps.1999.1276

A. Tamaki, A. Nakaoka, H. Maekawa, and F. Yamada, Spatial partitioning between species of the phytoplankton-feeding guild on an estuarine intertidal sand flat and its implication on habitat carrying capacity, Estuarine, Coastal and Shelf Science, vol.78, issue.4, pp.727-738, 2008.
DOI : 10.1016/j.ecss.2008.02.009

C. J. Ter-braak and I. C. Prentice, A Theory of Gradient Analysis, Adv Ecol Res, vol.34, pp.235-282, 2004.
DOI : 10.1016/S0065-2504(03)34003-6

P. Turchin and A. D. Taylor, Complex Dynamics in Ecological Time Series, Ecology, vol.73, issue.1, pp.289-305, 1992.
DOI : 10.2307/1938740

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.602.2628

R. E. Ulanowicz, Quantitative methods for ecological network analysis, Computational Biology and Chemistry, vol.28, issue.5-6, pp.321-339, 2004.
DOI : 10.1016/j.compbiolchem.2004.09.001

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

C. Walters, V. Christensen, and D. Pauly, Structuring dynamic models of exploited ecosystems from trophic mass-balance assessments, Reviews in Fish Biology and Fisheries, vol.7, issue.2, pp.139-172, 1997.
DOI : 10.1023/A:1018479526149

C. Walters, D. Pauly, and V. Christensen, Ecospace: Prediction of Mesoscale Spatial Patterns in Trophic Relationships of Exploited Ecosystems, with Emphasis on the Impacts of Marine Protected Areas, Ecosystems, vol.2, issue.6, pp.539-554, 1999.
DOI : 10.1007/s100219900101

R. B. Whitlatch, A. M. Lohrer, S. F. Thrush, R. D. Pridmore, J. E. Hewitt et al., Scale-dependent benthic recolonization dynamics: life stage-based dispersal and demographic consequences, Proceedings of the 32nd European Marine Biology Symposium, pp.16-22, 1998.
DOI : 10.1007/978-94-017-2864-5_18

P. Yodzis and S. Innes, Body Size and Consumer-Resource Dynamics, The American Naturalist, vol.139, issue.6, pp.1151-1175, 1992.
DOI : 10.1086/285380

F. G. Blanchet, P. Legendre, and D. Borcard, Modelling directional spatial processes in ecological data, Ecological Modelling, vol.215, issue.4, pp.325-336, 2008.
DOI : 10.1016/j.ecolmodel.2008.04.001

C. Bonnot-courtois and L. R. Lafond, Caractérisation et comportement des vases dans l'estuaire de la Rance, Rapport EDF EPHE, 1991.

Z. Botta-dukát, Rao's quadratic entropy as a measure of functional diversity based on multiple traits, Journal of Vegetation Science, vol.95, issue.5, pp.533-540, 2005.
DOI : 10.1034/j.1600-0706.2001.950119.x

I. Boulangeat, D. Georges, and W. Thuiller, FATE-HD: a spatially and temporally explicit integrated model for predicting vegetation structure and diversity at regional scale, Glob Change Biol, vol.20, pp.2368-2378, 2014.

I. Boulangeat, P. Philippe, S. Abdulhak, R. Douzet, L. Garraud et al., Improving plant functional groups for dynamic models of biodiversity: at the crossroads between functional and community ecology, Global Change Biology, vol.147, issue.11, pp.3464-3475, 2012.
DOI : 10.1111/j.1654-1103.2004.tb02316.x

J. Bremner, Species' traits and ecological functioning in marine conservation and management, Journal of Experimental Marine Biology and Ecology, vol.366, issue.1-2, pp.37-47, 2008.
DOI : 10.1016/j.jembe.2008.07.007

J. Bremner, O. A. Paramor, and C. L. Frid, Developing a methodology for incorporating ecological structure and functioning into designation of Special Areas of Conservation (SAC) in the 0-12 nautical mile zone, 2006.

J. Bremner, S. I. Rogers, and C. L. Frid, Methods for describing ecological functioning of marine benthic assemblages using biological traits analysis (BTA), Ecological Indicators, vol.6, issue.3, pp.609-622, 2006.
DOI : 10.1016/j.ecolind.2005.08.026

U. Brose, T. Jonsson, E. L. Berlow, P. Warren, C. Banasek-richter et al., CONSUMER???RESOURCE BODY-SIZE RELATIONSHIPS IN NATURAL FOOD WEBS, Ecology, vol.87, issue.10, pp.2411-2417, 2006.
DOI : 10.1086/285380

URL : https://researchonline.jcu.edu.au/3866/1/3866_Brose_et_al..._2006.pdf

A. Cardeccia, A. Marchini, A. Occhipinti-ambrogi, B. Galil, S. Gollasch et al., Assessing biological invasions in European Seas: Biological traits of the most widespread non-indigenous species, Estuarine, Coastal and Shelf Science, 2016.
DOI : 10.1016/j.ecss.2016.02.014

F. Chevenet, S. Dolédec, and D. Chessel, A fuzzy coding approach for the analysis of long-term ecological data, Freshwater Biology, vol.31, issue.3, pp.295-309, 1994.
DOI : 10.1007/BF00038688

K. R. Clarke, Non-parametric multivariate analyses of changes in community structure, Austral Ecology, vol.28, issue.1, pp.117-143, 1993.
DOI : 10.1007/BF00265008

A. Darr, M. Gogina, and M. L. Zettler, Functional changes in benthic communities along a salinity gradient??? a western Baltic case study, Journal of Sea Research, vol.85, pp.315-324, 2014.
DOI : 10.1016/j.seares.2013.06.003

N. Desroy, Les peuplements benthiques de substrats meubles du bassin maritime de la Rance Évolution de la biodiversité et effets de l'activité prédatrice de Nephtys hombergii (Annélide Polychète) PhD dissertation, 1998.

S. Dray and A. B. Dufour, The ade4 package: implementing the duality diagram for ecologists, J Stat Softw, vol.22, pp.1-20, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00434575

S. Dray, P. Legendre, and P. R. Peres-neto, Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM), Ecological Modelling, vol.196, issue.3-4, pp.483-493, 2006.
DOI : 10.1016/j.ecolmodel.2006.02.015

URL : https://hal.archives-ouvertes.fr/hal-00427943

N. Ferguson, C. R. White, and D. J. Marshall, Competition in benthic marine invertebrates: the unrecognized role of exploitative competition for oxygen, Ecology, vol.94, issue.1, pp.126-135, 2013.
DOI : 10.1890/10-2369.1

C. L. Frid, O. A. Paramor, S. Brockington, and J. Bremner, Incorporating ecological functioning into the designation and management of marine protected areas, Hydrobiologia, vol.216, issue.1, pp.69-79, 2008.
DOI : 10.1080/00364827.2001.10425526

C. Garcia, P. Chardy, J. Dewarumez, and J. Dauvin, Assessment of benthic ecosystem functioning through trophic web modelling: the example of the eastern basin of the English Channel and the Southern Bight of the North Sea, Marine Ecology, vol.1, issue.286, pp.72-86, 2011.
DOI : 10.1046/j.1467-2979.2000.00007.x

URL : https://hal.archives-ouvertes.fr/hal-00758157

E. Garnier, J. Cortez, G. Billès, M. Navas, C. Roumet et al., PLANT FUNCTIONAL MARKERS CAPTURE ECOSYSTEM PROPERTIES DURING SECONDARY SUCCESSION, Ecology, vol.85, issue.9, pp.2630-2637, 2004.
DOI : 10.1046/j.1469-8137.2002.00479.x

J. C. Gower, A General Coefficient of Similarity and Some of Its Properties, Biometrics, vol.27, issue.4, pp.857-871, 1971.
DOI : 10.2307/2528823

J. P. Grime, Benefits of plant diversity to ecosystems: immediate, filter and founder effects, Journal of Ecology, vol.51, issue.6, pp.902-910, 1998.
DOI : 10.1016/0169-5347(92)90006-W

J. P. Grime, ECOLOGY: Biodiversity and Ecosystem Function: The Debate Deepens, Science, vol.277, issue.5330, pp.1260-1261, 1997.
DOI : 10.1126/science.277.5330.1260

N. G. Hairston, . Jr, N. G. Hairston, and . Sr, Cause-Effect Relationships in Energy Flow, Trophic Structure, and Interspecific Interactions, The American Naturalist, vol.142, issue.3, pp.379-411, 1993.
DOI : 10.1086/285546

F. E. Harrell, . Jr, and C. Dupont, Hmisc: Harrell Miscellaneous. R package version 3, pp.15-15, 2015.

B. Hérault, Reconciling niche and neutrality through the Emergent Group approach, Perspectives in Plant Ecology, Evolution and Systematics, vol.9, issue.2, pp.71-78, 2007.
DOI : 10.1016/j.ppees.2007.08.001

P. Herman, J. Middelburg, J. Van-de-koppel, and C. Heip, Ecology of Estuarine Macrobenthos, Adv Ecol Res, vol.29, pp.195-240, 1999.
DOI : 10.1016/S0065-2504(08)60194-4

W. Hoeffding, A Non-Parametric Test of Independence, The Annals of Mathematical Statistics, vol.19, issue.4, pp.546-557, 1948.
DOI : 10.1214/aoms/1177730150

S. Hubbell, Neutral theory in community ecology and the hypothesis of functional equivalence, Functional Ecology, vol.84, issue.1, pp.166-172, 2005.
DOI : 10.1017/CBO9780511542237

T. C. Ings, J. M. Montoya, J. Bascompte, N. Blüthgen, L. Brown et al., Review: Ecological networks - beyond food webs, Journal of Animal Ecology, vol.3, issue.1, pp.253-269, 2009.
DOI : 10.1017/CBO9780511611223.007

F. C. James and C. E. Mcculloch, Multivariate Analysis in Ecology and Systematics: Panacea or Pandora's Box?, Annual Review of Ecology and Systematics, vol.21, issue.1, pp.129-166, 1990.
DOI : 10.1146/annurev.es.21.110190.001021

K. Jax, Function and ???functioning??? in ecology: what does it mean?, Oikos, vol.96, issue.3, pp.641-648, 2005.
DOI : 10.1007/978-3-642-58001-7_13

W. Jetz, C. Carbone, J. Fulford, and J. H. Brown, The Scaling of Animal Space Use, Science, vol.306, issue.5694, pp.266-268, 2004.
DOI : 10.1126/science.1102138

H. Jimenez, P. Dumas, D. Mouillot, L. Bigot, and J. Ferraris, Harvesting effects on functional structure and composition of tropical invertebrate assemblages, ICES Journal of Marine Science: Journal du Conseil, vol.73, issue.2, pp.420-428, 2015.
DOI : 10.1093/icesjms/fsv179

S. Kéfi, E. L. Berlow, E. A. Wieters, S. A. Navarrete, O. L. Petchey et al., More than a meal??? integrating non-feeding interactions into food webs, Ecology Letters, vol.139, issue.4, pp.291-300, 2012.
DOI : 10.1086/285380

R. Kirby and C. Retière, Comparing environmental effects of Rance and Severn barrages, Proceedings of the Institution of Civil Engineers - Maritime Engineering, vol.162, issue.1, pp.11-26, 2009.
DOI : 10.1680/maen.2009.162.1.11

W. H. Kruskal and W. A. Wallis, Use of Ranks in One-Criterion Variance Analysis, Journal of the American Statistical Association, vol.3, issue.260, pp.583-621, 1952.
DOI : 10.2307/3001946

S. Lavorel, S. Mcintyre, J. Landsberg, and T. D. Forbes, Plant functional classifications: from general groups to specific groups based on response to disturbance, Trends in Ecology & Evolution, vol.12, issue.12, pp.474-478, 1997.
DOI : 10.1016/S0169-5347(97)01219-6

E. Laliberté, P. Legendre, and B. Shipley, FD: measuring functional diversity from multiple traits, and other tools for functional ecology. R package version 1, pp.0-12, 2014.

P. Legendre and O. Gauthier, Statistical methods for temporal and space-time analysis of community composition data, Proceedings of the Royal Society B: Biological Sciences, vol.14, issue.1, 2014.
DOI : 10.1111/j.1461-0248.2010.01552.x

URL : https://hal.archives-ouvertes.fr/hal-00948693

M. Maechler, P. Rousseeuw, A. Struyf, M. Hubert, and K. Hornik, cluster: cluster analysis basics and extensions, 2013.

N. W. Mason, D. Mouillot, W. G. Lee, and J. B. Wilson, Functional richness, functional evenness and functional divergence: the primary components of functional diversity, Oikos, vol.86, issue.1, pp.112-118, 2005.
DOI : 10.1016/B0-12-226865-2/00132-2

E. L. Mclean and H. R. Lasker, Height matters: position above the substratum influences the growth of two demosponge species, Marine Ecology, vol.54, issue.1, pp.122-129, 2013.
DOI : 10.3354/meps054257

B. A. Menge, Indirect Effects in Marine Rocky Intertidal Interaction Webs: Patterns and Importance, Ecological Monographs, vol.65, issue.1, pp.21-74, 1995.
DOI : 10.2307/2937158

A. Muntadas, S. De-juan, and M. Demestre, Assessing functional redundancy in chronically trawled benthic communities, Ecological Indicators, vol.61, pp.882-892, 2016.
DOI : 10.1016/j.ecolind.2015.10.041

M. Ortiz and M. Wolff, Dynamical simulation of mass-balance trophic models for benthic communities of north-central Chile: assessment of resilience time under alternative management scenarios, Ecological Modelling, vol.148, issue.3, pp.277-291, 2002.
DOI : 10.1016/S0304-3800(01)00454-9

S. Pavoine, S. Ollier, and D. Pontier, Measuring diversity from dissimilarities with Rao's quadratic entropy: Are any dissimilarities suitable?, Theoretical Population Biology, vol.67, issue.4, pp.231-239, 2005.
DOI : 10.1016/j.tpb.2005.01.004

URL : https://hal.archives-ouvertes.fr/hal-00427714

T. H. Pearson, Functional group ecology in soft-sediment marine benthos: the role of bioturbation, Oceanogr Mar Biol, vol.39, pp.233-267, 2001.

O. L. Petchey and K. J. Gaston, Functional diversity: back to basics and looking forward, Ecology Letters, vol.81, issue.6, pp.741-758, 2006.
DOI : 10.1016/0038-0717(94)90131-7

M. H. Posey, Influence of relative mobilities on the composition of benthic communities, Marine Ecology Progress Series, vol.39, pp.99-104, 1987.
DOI : 10.3354/meps039099

R. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2015.

H. Reiss, S. Knäuper, and I. Kröncke, Invertebrate associations with gastropod shells inhabited by Pagurus??bernhardus (Paguridae) ??? secondary hard substrate increasing biodiversity??in North Sea soft???bottom communities, Sarsia, vol.31, issue.3, pp.404-415, 2003.
DOI : 10.1007/BF03043036

C. Retière, Tidal power and the aquatic environment of La Rance, Biological Journal of the Linnean Society, vol.51, issue.1-2, pp.25-36, 1994.
DOI : 10.1111/j.1095-8312.1994.tb00941.x

L. A. Robinson, S. P. Greenstreet, H. Reiss, R. Callaway, J. Craeymeersch et al., Length???weight relationships of 216 North Sea benthic invertebrates and fish, Journal of the Marine Biological Association of the United Kingdom, vol.63, issue.01, pp.95-104, 2010.
DOI : 10.1111/j.1365-2656.2006.01180.x

URL : http://edepot.wur.nl/134604

J. S. Rosenfeld, Functional redundancy in ecology and conservation, Oikos, vol.60, issue.1, pp.156-162, 2002.
DOI : 10.1046/j.1523-1739.1995.09040747.x

V. M. Savage, J. F. Gillooly, J. H. Brown, G. B. West, and E. L. Charno, Effects of Body Size and Temperature on Population Growth, The American Naturalist, vol.163, issue.3, pp.429-441, 2004.
DOI : 10.1086/381872

C. Scherer, F. Jeltsch, V. Grimm, and N. Blaum, Merging trait-based and individual-based modelling: An animal functional type approach to explore the responses of birds to climatic and land use changes in semi-arid African savannas, Ecological Modelling, vol.326, pp.75-89, 2016.
DOI : 10.1016/j.ecolmodel.2015.07.005

R. R. Sokal and C. D. Michener, A statistical method for evaluating systematic relationships, Univ Kans Sci Bull, vol.28, pp.1409-1438, 1958.

W. J. Sutherland, R. P. Freckleton, H. C. Godfray, S. R. Beissinger, T. Benton et al., Identification of 100 fundamental ecological questions, Journal of Ecology, vol.3, issue.3, pp.58-67, 2013.
DOI : 10.1111/j.2041-210X.2011.00164.x

URL : http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12025/pdf

D. S. Srivastava and M. Vellend, Biodiversity-Ecosystem Function Research: Is It Relevant to Conservation?, Annual Review of Ecology, Evolution, and Systematics, vol.36, issue.1, pp.267-294, 2005.
DOI : 10.1146/annurev.ecolsys.36.102003.152636

C. J. Ter-braak and I. C. Prentice, A Theory of Gradient Analysis, Adv Ecol Res, vol.34, pp.235-282, 2004.
DOI : 10.1016/S0065-2504(03)34003-6

D. Tilman, Constraints and Tradeoffs: Toward a Predictive Theory of Competition and Succession, Oikos, vol.58, issue.1, pp.3-15, 1990.
DOI : 10.2307/3565355

D. Tilman, Resources: A Graphical-Mechanistic Approach to Competition and Predation, The American Naturalist, vol.116, issue.3, pp.362-393, 1980.
DOI : 10.1086/283633

A. Törnroos and E. Bonsdorff, Developing the multitrait concept for functional diversity: lessons from a system rich in functions but poor in species, Ecological Applications, vol.22, issue.8, pp.2221-2236, 2012.
DOI : 10.1126/science.1132294

E. H. Tyler, P. J. Somerfield, E. V. Berghe, J. Bremner, E. Jackson et al., Extensive gaps and biases in our knowledge of a well-known fauna: implications for integrating biological traits into macroecology, Global Ecology and Biogeography, vol.13, issue.9, pp.922-934, 2012.
DOI : 10.1111/j.1461-0248.2010.01444.x

R. E. Ulanowicz, Quantitative methods for ecological network analysis, Computational Biology and Chemistry, vol.28, issue.5-6, pp.321-339, 2004.
DOI : 10.1016/j.compbiolchem.2004.09.001

P. Van-der-linden, A. Marchini, M. Dolbeth, J. Patrício, H. Veríssimo et al., The performance of trait-based indices in an estuarine environment, Ecological Indicators, vol.61, pp.378-389, 2016.
DOI : 10.1016/j.ecolind.2015.09.039

B. H. Walker, Biodiversity and Ecological Redundancy, Conservation Biology, vol.44, issue.1, pp.18-23, 1992.
DOI : 10.1016/0006-3207(91)90030-D

S. Woodin, R. Marinelli, and D. Lincoln, Allelochemical inhibition of recruitment in a sedimentary assemblage, Journal of Chemical Ecology, vol.107, issue.3, pp.517-530, 1993.
DOI : 10.1007/BF00994322

P. Yodzis and S. Innes, Body Size and Consumer-Resource Dynamics, The American Naturalist, vol.139, issue.6, pp.1151-1175, 1992.
DOI : 10.1086/285380

N. Alexandridis, C. Bacher, N. Desroy, and F. Jean, Building functional groups of marine benthic macroinvertebrates on the basis of general community assembly mechanisms, Journal of Sea Research, vol.121, pp.59-70, 2017.
DOI : 10.1016/j.seares.2017.01.007

URL : https://hal.archives-ouvertes.fr/hal-01510353

P. Amarasekare, Competitive coexistence in spatially structured environments: a synthesis, Ecology Letters, vol.158, issue.12, pp.1109-1122, 2003.
DOI : 10.1093/biomet/38.1-2.196

URL : http://onlinelibrary.wiley.com/doi/10.1046/j.1461-0248.2003.00530.x/pdf

T. M. Blackburn and K. J. Gaston, Animal body size distributions: patterns, mechanisms and implications, Trends in Ecology & Evolution, vol.9, issue.12, pp.471-474, 1994.
DOI : 10.1016/0169-5347(94)90311-5

C. Bonnot-courtois, Evolution de la répartition des sédiments dans l'estuaire de la Rance, 1883-1994. Atlas, p.29, 1997.

C. Bonnot-courtois and L. R. Lafond, Caractérisation et comportement des vases dans l'estuaire de la Rance, Rapport EDF. EPHE, 1991.

I. Boulangeat, P. Philippe, S. Abdulhak, R. Douzet, L. Garraud et al., Improving plant functional groups for dynamic models of biodiversity: at the crossroads between functional and community ecology, Global Change Biology, vol.147, issue.11, pp.3464-3475, 2012.
DOI : 10.1111/j.1654-1103.2004.tb02316.x

U. Brose, T. Jonsson, E. L. Berlow, P. Warren, C. Banasek-richter et al., CONSUMER???RESOURCE BODY-SIZE RELATIONSHIPS IN NATURAL FOOD WEBS, Ecology, vol.87, issue.10, pp.2411-2417, 2006.
DOI : 10.1086/285380

URL : https://researchonline.jcu.edu.au/3866/1/3866_Brose_et_al..._2006.pdf

U. Brose, R. J. Williams, and N. D. Martinez, Allometric scaling enhances stability in complex food webs, Ecology Letters, vol.86, issue.11, pp.1228-1236, 2006.
DOI : 10.1086/285380

B. J. Cardinale, J. E. Duffy, A. Gonzalez, D. U. Hooper, C. Perrings et al., Biodiversity loss and its impact on humanity, Nature, vol.4, issue.7401, pp.59-67
DOI : 10.1016/j.cosust.2012.01.007

URL : http://pub.epsilon.slu.se/10240/7/wardle_d_etal_130415.pdf

M. P. Carey, P. S. Levin, H. Townsend, T. J. Minello, G. R. Sutton et al., Characterizing coastal foodwebs with qualitative links to bridge the gap between the theory and the practice of ecosystem-based management, ICES Journal of Marine Science, vol.71, issue.3, pp.713-724, 2014.
DOI : 10.1093/icesjms/fst012

J. M. Chase and M. A. Leibold, Ecological niches: linking classical and contemporary approaches, 2003.
DOI : 10.7208/chicago/9780226101811.001.0001

P. Chesson, Mechanisms of Maintenance of Species Diversity, Annual Review of Ecology and Systematics, vol.31, issue.1, pp.343-366, 2000.
DOI : 10.1146/annurev.ecolsys.31.1.343

J. E. Cohen, S. L. Pimm, P. Yodzis, and J. Saldaña, Body Sizes of Animal Predators and Animal Prey in Food Webs, The Journal of Animal Ecology, vol.62, issue.1, pp.67-78, 1993.
DOI : 10.2307/5483

J. H. Connell, On the Prevalence and Relative Importance of Interspecific Competition: Evidence from Field Experiments, The American Naturalist, vol.122, issue.5, pp.661-696, 1983.
DOI : 10.1086/284165

J. M. Dambacher, D. T. Brewer, D. M. Dennis, M. Macintyre, and S. Foale, Qualitative Modelling of Gold Mine Impacts on Lihir Island's Socioeconomic System and Reef-Edge Fish Community, Environmental Science & Technology, vol.41, issue.2, pp.555-562, 2007.
DOI : 10.1021/es0610333

J. M. Dambacher, H. W. Li, and P. A. Rossignol, RELEVANCE OF COMMUNITY STRUCTURE IN ASSESSING INDETERMINACY OF ECOLOGICAL PREDICTIONS, Ecology, vol.83, issue.5, pp.1372-1385, 2002.
DOI : 10.2307/1940449

M. R. Lancaster and J. , Length?weight relationships of 216 North Sea benthic invertebrates and fish, J Mar Biol Assoc UK, vol.90, pp.95-104, 2010.

V. M. Savage, J. F. Gillooly, J. H. Brown, G. B. West, and E. L. Charnov, Effects of Body Size and Temperature on Population Growth, The American Naturalist, vol.163, issue.3, pp.429-441, 2004.
DOI : 10.1086/381872

M. Schratzberger and P. Larcombe, The Role of the Sedimentary Regime in Shaping the Distribution of Subtidal Sandbank Environments and the Associated Meiofaunal Nematode Communities: An Example from the Southern North Sea, PLoS ONE, vol.102, issue.10, 2014.
DOI : 10.1371/journal.pone.0109445.s002

P. V. Snelgrove and C. A. Butman, Animal-sediment relationships revisited: cause versus effect, Oceanogr Mar Biol, vol.32, pp.111-177, 1994.

W. J. Sutherland, R. P. Freckleton, H. C. Godfray, S. R. Beissinger, T. Benton et al., Identification of 100 fundamental ecological questions, Journal of Ecology, vol.3, issue.3, pp.58-67, 2013.
DOI : 10.1111/j.2041-210X.2011.00164.x

URL : http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12025/pdf

J. R. Svensson and D. J. Marshall, Limiting resources in sessile systems: food enhances diversity and growth of suspension feeders despite available space, Ecology, vol.96, issue.3, pp.819-827, 2015.
DOI : 10.1006/jmps.1999.1276

D. Tilman, Resources: A Graphical-Mechanistic Approach to Competition and Predation, The American Naturalist, vol.116, issue.3, pp.362-393, 1980.
DOI : 10.1086/283633

D. Tilman, Constraints and Tradeoffs: Toward a Predictive Theory of Competition and Succession, Oikos, vol.58, issue.1, pp.3-15, 1990.
DOI : 10.2307/3565355

N. Volkenborn, D. M. Robertson, and K. Reise, Sediment destabilizing and stabilizing bio-engineers on tidal flats: cascading effects of experimental exclusion, Helgoland Marine Research, vol.54, issue.1, pp.27-35, 2009.
DOI : 10.1093/icb/19.4.1029

M. Wahl, Marine epibiosis. I. Fouling and antifouling: some basic aspects, Marine Ecology Progress Series, vol.58, pp.175-189, 1989.
DOI : 10.3354/meps058175

URL : http://oceanrep.geomar.de/23175/1/art_10.1007_BF00323545.pdf

M. Wahl and O. Mark, The predominantly facultative nature of epibiosis: experimental and observational evidence, Marine Ecology Progress Series, vol.187, pp.59-66, 1999.
DOI : 10.3354/meps187059

G. Woodward, B. Ebenman, M. Emmerson, J. M. Montoya, J. M. Olesen et al., Body size in ecological networks, Trends in Ecology & Evolution, vol.20, issue.7, pp.402-409, 2005.
DOI : 10.1016/j.tree.2005.04.005

N. Alexandridis, C. Bacher, N. Desroy, and F. Jean, Building functional groups of marine benthic macroinvertebrates on the basis of general community assembly mechanisms, Journal of Sea Research, vol.121, pp.59-70, 2017.
DOI : 10.1016/j.seares.2017.01.007

URL : https://hal.archives-ouvertes.fr/hal-01510353

C. Bonnot-courtois, Evolution de la répartition des sédiments dans l'estuaire de la Rance, 1883-1994. Atlas, p.29, 1997.

D. Borcard, F. Gillet, and P. Legendre, Numerical Ecology with R, 2011.
DOI : 10.1007/978-1-4419-7976-6

URL : https://hal.archives-ouvertes.fr/hal-00530195

I. Boulangeat, P. Philippe, S. Abdulhak, R. Douzet, L. Garraud et al., Improving plant functional groups for dynamic models of biodiversity: at the crossroads between functional and community ecology, Global Change Biology, vol.147, issue.11, pp.3464-3475, 2012.
DOI : 10.1111/j.1654-1103.2004.tb02316.x

U. Brose, T. Jonsson, E. L. Berlow, P. Warren, C. Banasek-richter et al., CONSUMER???RESOURCE BODY-SIZE RELATIONSHIPS IN NATURAL FOOD WEBS, Ecology, vol.87, issue.10, pp.2411-2417, 2006.
DOI : 10.1086/285380

URL : https://researchonline.jcu.edu.au/3866/1/3866_Brose_et_al..._2006.pdf

U. Brose, R. J. Williams, and N. D. Martinez, Allometric scaling enhances stability in complex food webs, Ecology Letters, vol.86, issue.11, pp.1228-1236, 2006.
DOI : 10.1086/285380

C. A. Butman, M. Fréchette, W. R. Geyer, and V. R. Starczak, L. as a function of boundary-layerflow, Limnology and Oceanography, vol.39, issue.7, pp.1755-1768, 1994.
DOI : 10.4319/lo.1994.39.7.1755

J. E. Cohen, S. L. Pimm, P. Yodzis, and J. Saldaña, Body Sizes of Animal Predators and Animal Prey in Food Webs, The Journal of Animal Ecology, vol.62, issue.1, pp.67-78, 1993.
DOI : 10.2307/5483

J. Côté, J. H. Himmelman, and M. R. Claereboudt, Separating effects of limited food and space on growth of the giant scallop Placopecten magellanicus in suspended culture, Marine Ecology Progress Series, vol.106, pp.85-91, 1994.
DOI : 10.3354/meps106085

D. L. Deangelis and W. M. Mooij, Individual-Based Modeling of Ecological and Evolutionary Processes, Annual Review of Ecology, Evolution, and Systematics, vol.36, issue.1, pp.147-168, 2005.
DOI : 10.1146/annurev.ecolsys.36.102003.152644

N. Desroy, Les peuplements benthiques de substrats meubles du bassin maritime de la Rance Évolution de la biodiversité et effets de l'activité prédatrice de Nephtys hombergii (Annélide Polychète) PhD Dissertation, 1998.

C. Ellien, É. Thiebaut, A. Barnay, J. Dauvin, F. Gentil et al., The influence of variability in larval dispersal on the dynamics of a marine metapopulation in the eastern Channel, Oceanologica Acta, vol.23, issue.4, pp.423-442, 2000.
DOI : 10.1016/S0399-1784(00)00136-5

S. Fraschetti, A. Giangrande, A. Terlizzi, and F. Boero, Pre- and post-settlement events in benthic community dynamics, Oceanologica Acta, vol.25, issue.6, pp.285-295, 2002.
DOI : 10.1016/S0399-1784(02)01194-5

URL : http://archimer.ifremer.fr/doc/00322/43295/43031.pdf

M. Fréchette, C. A. Butman, and W. R. Geyer, The importance of boundary-layer flows in supplying phytoplankton to the benthic suspension feeder, Mytilus edulis L., Limnology and Oceanography, vol.34, issue.1, pp.19-36, 1989.
DOI : 10.4319/lo.1989.34.1.0019

L. A. Gosselin and P. Y. Qian, Juvenile mortality in benthic marine invertebrates, Marine Ecology Progress Series, vol.146, pp.265-282, 1997.
DOI : 10.3354/meps146265

V. Grimm, U. Berger, F. Bastiansen, S. Eliassen, V. Ginot et al., A standard protocol for describing individual-based and agent-based models, Ecological Modelling, vol.198, issue.1-2, pp.115-126, 2006.
DOI : 10.1016/j.ecolmodel.2006.04.023

V. Grimm, U. Berger, D. L. Deangelis, J. G. Polhill, J. Giske et al., The ODD protocol: A review and first update, Ecological Modelling, vol.221, issue.23, pp.2760-2768, 2010.
DOI : 10.1016/j.ecolmodel.2010.08.019

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.417.2226

B. Hérault, Reconciling niche and neutrality through the Emergent Group approach, Perspectives in Plant Ecology, Evolution and Systematics, vol.9, issue.2, pp.71-78, 2007.
DOI : 10.1016/j.ppees.2007.08.001

P. Herman, J. Middelburg, J. Van-de-koppel, and C. Heip, Ecology of Estuarine Macrobenthos, Adv Ecol Res, vol.29, pp.195-240, 1999.
DOI : 10.1016/S0065-2504(08)60194-4

R. J. Hijmans, raster: Geographic Data Analysis and Modeling, 2016.

A. Hjorth, B. Head, and U. Wilensky, LevelSpace NetLogo extension, 2015.

S. P. Hubbell, Neutral theory in community ecology and the hypothesis of functional equivalence, Functional Ecology, vol.84, issue.1, pp.166-172, 2005.
DOI : 10.1017/CBO9780511542237

H. L. Hunt and R. E. Scheibling, Role of early post-settlement mortality in recruitment of benthic marine invertebrates, Marine Ecology Progress Series, vol.155, pp.269-301, 1997.
DOI : 10.3354/meps155269

J. Ingels, S. L. Dashfield, P. J. Somerfield, S. Widdicombe, and M. C. Austen, Interactions between multiple large macrofauna species and nematode communities ??? Mechanisms for indirect impacts of trawling disturbance, Journal of Experimental Marine Biology and Ecology, vol.456, pp.41-49, 2014.
DOI : 10.1016/j.jembe.2014.03.009

E. K. Kupriyanova, E. Nishi, H. A. Ten-hove, and A. V. Rzhavsky, Life-history patterns in serpulimorph polychaetes: ecological and evolutionary perspectives, 2001.
DOI : 10.1007/978-94-017-0655-1_11

P. Legendre and M. De-cáceres, Beta diversity as the variance of community data: dissimilarity coefficients and partitioning, Ecology Letters, vol.72, issue.8, pp.951-963, 2013.
DOI : 10.2307/2259551

P. Legendre and L. Legendre, Numerical ecology: second English edition, 1998.

J. Lord and R. Whitlatch, Predicting competitive shifts and responses to climate change based on latitudinal distributions of species assemblages, Ecology, vol.96, issue.5, pp.1264-1274, 2015.
DOI : 10.1890/14-0403.1.sm

J. Oksanen, G. Blanchet, R. Kindt, P. Legendre, P. R. Minchin et al., vegan: Community Ecology Package, 2015.

E. B. Olafsson, C. H. Peterson, and W. G. Ambrose, Does recruitment limitation structure populations and communities of macroinvertebrates in marine soft sediments ? the relative significance of presettlement and postsettlement processes, Oceanogr Mar Biol, vol.32, pp.65-109, 1994.

J. Pineda, N. B. Reyns, and V. R. Starczak, Complexity and simplification in understanding recruitment in benthic populations, Population Ecology, vol.30, issue.1, pp.17-32, 2009.
DOI : 10.4319/lo.2006.51.5.1982

M. H. Posey, Influence of relative mobilities on the composition of benthic communities, Marine Ecology Progress Series, vol.39, pp.99-104, 1987.
DOI : 10.3354/meps039099

R. Team, R: a language and environment for statistical computing, Rproject .org/. R Foundation for Statistical Computing, 2015.

P. Snelgrove and C. Butman, Animal-sediment relationships revisited: cause versus effect, Oceanogr Mar Biol, vol.32, pp.111-177, 1994.

J. R. Svensson and D. J. Marshall, Limiting resources in sessile systems: food enhances diversity and growth of suspension feeders despite available space, Ecology, vol.96, issue.3, pp.819-827, 2015.
DOI : 10.1006/jmps.1999.1276

K. I. Ugland, J. S. Gray, and K. E. Ellingsen, The species-accumulation curve and estimation of species richness, Journal of Animal Ecology, vol.71, issue.5, pp.888-897, 2003.
DOI : 10.1017/CBO9780511623387

T. Brey, An empirical model for estimating aquatic invertebrate respiration, Methods in Ecology and Evolution, vol.212, issue.1, pp.92-101, 2010.
DOI : 10.1093/icb/11.3.571

URL : http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2009.00008.x/pdf

J. H. Brown, J. F. Gillooly, A. P. Allen, V. M. Savage, and G. B. West, TOWARD A METABOLIC THEORY OF ECOLOGY, Ecology, vol.85, issue.7, pp.1771-1789, 2004.
DOI : 10.1073/pnas.012579799

P. A. Cipriotti, T. Wiegand, S. Pütz, N. J. Bartoloni, and J. M. Paruelo, Nonparametric upscaling of stochastic simulation models using transition matrices, Methods in Ecology and Evolution, vol.70, issue.3, pp.313-322, 2015.
DOI : 10.1007/1-4020-4663-4

A. J. Constable, Ecology of benthic macro-invertebrates in soft-sediment environments: A review of progress towards quantitative models and predictions, Austral Ecology, vol.175, issue.4, pp.452-476, 1999.
DOI : 10.1093/icb/31.6.797

J. M. Dambacher, H. W. Li, and P. A. Rossignol, RELEVANCE OF COMMUNITY STRUCTURE IN ASSESSING INDETERMINACY OF ECOLOGICAL PREDICTIONS, Ecology, vol.83, issue.5, pp.1372-1385, 2002.
DOI : 10.2307/1940449

B. Dauwe, P. M. Herman, and C. H. Heip, Community structure and bioturbation potential of macrofauna at four North Sea stations with contrasting food supply, Marine Ecology Progress Series, vol.173, pp.67-83, 1998.
DOI : 10.3354/meps173067

D. L. Deangelis and W. M. Mooij, Individual-Based Modeling of Ecological and Evolutionary Processes, Annual Review of Ecology, Evolution, and Systematics, vol.36, issue.1, pp.147-168, 2005.
DOI : 10.1146/annurev.ecolsys.36.102003.152644

M. Denny and L. Benedetti-cecchi, Scaling Up in Ecology: Mechanistic Approaches, Annual Review of Ecology, Evolution, and Systematics, vol.43, issue.1, pp.1-22, 2012.
DOI : 10.1146/annurev-ecolsys-102710-145103

N. Desroy, Les peuplements benthiques de substrats meubles du bassin maritime de la Rance Évolution de la biodiversité et effets de l'activité prédatrice de Nephtys hombergii (Annélide Polychète) PhD dissertation, 1998.

S. Dray, P. Choler, S. Dolédec, P. R. Peres-neto, W. Thuiller et al., Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation, Ecology, vol.95, issue.1, pp.14-21, 2014.
DOI : 10.1111/j.1654-1103.2011.01342.x

URL : https://hal.archives-ouvertes.fr/halsde-00942845

A. Drogoul, E. Amouroux, P. Caillou, B. Gaudou, A. Grignard et al., GAMA: multi-level and complex environment for agent-based models and simulations, Proceedings of the 2013 international conference on Autonomous agents and multi-agent systems, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00834498

M. R. Evans, V. Grimm, K. Johst, T. Knuuttila, R. De-langhe et al., Do simple models lead to generality in ecology?, Trends in Ecology & Evolution, vol.28, issue.10, pp.578-583, 2013.
DOI : 10.1016/j.tree.2013.05.022

URL : http://qmro.qmul.ac.uk/xmlui/handle/123456789/10738

C. L. Frid, O. A. Paramor, S. Brockington, and J. Bremner, Incorporating ecological functioning into the designation and management of marine protected areas, Hydrobiologia, vol.216, issue.1, pp.69-79, 2008.
DOI : 10.1080/00364827.2001.10425526

A. Grignard, P. Taillandier, B. Gaudou, D. A. Vo, N. Q. Huynh et al., GAMA 1.6: Advancing the Art of Complex Agent-Based Modeling and Simulation, PRIMA 2013: Principles and Practice of Multi-Agent Systems: 16th International Conference, 2006.
DOI : 10.1007/978-3-642-44927-7_9

URL : https://hal.archives-ouvertes.fr/hal-00932406

B. Hérault, Reconciling niche and neutrality through the Emergent Group approach, Perspectives in Plant Ecology, Evolution and Systematics, vol.9, issue.2, pp.71-78, 2007.
DOI : 10.1016/j.ppees.2007.08.001

P. Herman, J. Middelburg, J. Van-de-koppel, and C. Heip, Ecology of Estuarine Macrobenthos, Adv Ecol Res, vol.29, pp.195-240, 1999.
DOI : 10.1016/S0065-2504(08)60194-4

F. Jean, Modélisation à l'état stable des transferts de Carbone dans le réseau trophique benthique de la rade de Brest (France) PhD dissertation, 1994.

S. Kéfi, E. L. Berlow, E. A. Wieters, S. A. Navarrete, O. L. Petchey et al., More than a meal??? integrating non-feeding interactions into food webs, Ecology Letters, vol.139, issue.4, pp.291-300, 2012.
DOI : 10.1086/285380

J. M. Kneitel and J. M. Chase, Trade-offs in community ecology: linking spatial scales and species coexistence, Ecology Letters, vol.82, issue.1, pp.69-80, 2004.
DOI : 10.1146/annurev.ecolsys.32.081501.114006

A. Kubicek, F. Jopp, B. Breckling, C. Lange, and H. Reuter, Context-oriented model validation of individual-based models in ecology: A hierarchically structured approach to validate qualitative, compositional and quantitative characteristics, Ecological Complexity, vol.22, pp.178-191, 2015.
DOI : 10.1016/j.ecocom.2015.03.005

R. Levins, The strategy of model building in population biology, Am Sci, vol.54, pp.421-431, 1966.

Q. Liu, P. M. Herman, W. M. Mooij, J. Huisman, M. Scheffer et al., Pattern formation at multiple spatial scales drives the resilience of mussel bed ecosystems, Nature Communications, vol.117, p.5234, 2014.
DOI : 10.1007/s00285-013-0689-z

K. G. Lyons, C. A. Brigham, B. H. Traut, and M. W. Schwartz, Rare Species and Ecosystem Functioning, Conservation Biology, vol.51, issue.4, pp.1019-1024, 2005.
DOI : 10.1641/0006-3568(2001)051[1005:DBWSMA]2.0.CO;2

B. T. Martin, T. Jager, R. M. Nisbet, T. G. Preuss, and V. Grimm, Predicting Population Dynamics from the Properties of Individuals: A Cross-Level Test of Dynamic Energy Budget Theory, The American Naturalist, vol.181, issue.4, pp.506-519, 2013.
DOI : 10.1086/669904

A. Morozov and J. Poggiale, From spatially explicit ecological models to mean-field dynamics: The state of the art and perspectives, Ecological Complexity, vol.10, pp.1-11, 2012.
DOI : 10.1016/j.ecocom.2012.04.001

D. Mouillot, D. R. Bellwood, C. Baraloto, J. Chave, R. Galzin et al., Rare Species Support Vulnerable Functions in High-Diversity Ecosystems, PLoS Biology, vol.2, issue.5, 2013.
DOI : 10.1371/journal.pbio.1001569.s004

URL : https://hal.archives-ouvertes.fr/hal-00912633

M. J. North, N. T. Collier, J. Ozik, E. R. Tatara, C. M. Macal et al., Complex adaptive systems modeling with Repast Simphony, Complex Adaptive Systems Modeling, vol.1, issue.1, 2013.
DOI : 10.1002/cplx.20093

D. P. Peters, B. T. Bestelmeyer, and M. G. Turner, Cross???Scale Interactions and Changing Pattern???Process Relationships: Consequences for System Dynamics, Cross?Scale Interactions and Changing Pattern?Process Relationships: Consequences for System Dynamics, pp.790-796, 2007.
DOI : 10.1007/0-387-24091-8_2

URL : https://naldc.nal.usda.gov/naldc/download.xhtml?id=15145&content=PDF

M. H. Posey, Influence of relative mobilities on the composition of benthic communities, Marine Ecology Progress Series, vol.39, pp.99-104, 1987.
DOI : 10.3354/meps039099

S. F. Railsback, S. L. Lytinen, and S. K. Jackson, Agent-based Simulation Platforms: Review and Development Recommendations, SIMULATION, vol.99, issue.3, pp.609-623, 2006.
DOI : 10.1073/pnas.072079499

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.7310

C. Scherer, F. Jeltsch, V. Grimm, and N. Blaum, Merging trait-based and individual-based modelling: An animal functional type approach to explore the responses of birds to climatic and land use changes in semi-arid African savannas, Ecological Modelling, vol.326, pp.75-89, 2016.
DOI : 10.1016/j.ecolmodel.2015.07.005

J. C. Sleeman, G. S. Boggs, B. C. Radford, and G. A. Kendrick, Using Agent-Based Models to Aid Reef Restoration: Enhancing Coral Cover and Topographic Complexity through the Spatial Arrangement of Coral Transplants, Restoration Ecology, vol.42, issue.4, pp.685-694, 2005.
DOI : 10.1016/S0025-326X(03)00040-7

D. S. Srivastava and M. Vellend, Biodiversity-Ecosystem Function Research: Is It Relevant to Conservation?, Annual Review of Ecology, Evolution, and Systematics, vol.36, issue.1, pp.267-294, 2005.
DOI : 10.1146/annurev.ecolsys.36.102003.152636

R. A. Stillman, S. F. Railsback, J. Giske, U. Berger, and V. Grimm, Making Predictions in a Changing World: The Benefits of Individual-Based Ecology, BioScience, vol.65, issue.2, pp.140-150, 2015.
DOI : 10.1093/biosci/biu192

C. Swinerd and K. R. Mcnaught, Design classes for hybrid simulations involving agent-based and system dynamics models, Simulation Modelling Practice and Theory, vol.25, pp.118-133, 2012.
DOI : 10.1016/j.simpat.2011.09.002

URL : https://dspace.lib.cranfield.ac.uk/bitstream/1826/8096/1/HybridSimulationDesignClasses_SwinerdMcNaught_PreprintFinal.pdf

S. F. Thrush, V. J. Cummings, P. K. Dayton, R. Ford, J. Grant et al., Matching the outcome of small-scale density manipulation experiments with larger scale patterns, Journal of Experimental Marine Biology and Ecology, vol.216, issue.1-2, pp.153-169, 1997.
DOI : 10.1016/S0022-0981(97)00094-4

D. Tilman, Resources: A Graphical-Mechanistic Approach to Competition and Predation, The American Naturalist, vol.116, issue.3, pp.362-393, 1980.
DOI : 10.1086/283633

C. Van-colen, F. Montserrat, M. Vincx, P. M. Herman, T. Ysebaert et al., Macrobenthic recovery from hypoxia in an estuarine tidal mudflat, Marine Ecology Progress Series, vol.372, pp.31-42, 2008.
DOI : 10.3354/meps07640

N. Volkenborn, D. M. Robertson, and K. Reise, Sediment destabilizing and stabilizing bio-engineers on tidal flats: cascading effects of experimental exclusion, Helgoland Marine Research, vol.54, issue.1, pp.27-35, 2009.
DOI : 10.1093/icb/19.4.1029

A. T. Yñiguez, J. W. Mcmanus, and D. L. Deangelis, Allowing macroalgae growth forms to emerge: Use of an agent-based model to understand the growth and spread of macroalgae in Florida coral reefs, with emphasis on Halimeda tuna, Ecological Modelling, vol.216, issue.1, pp.60-74, 2008.
DOI : 10.1016/j.ecolmodel.2008.04.016

T. Ysebaert and P. M. Herman, Spatial and temporal variation in benthic macrofauna and relationships with environmental variables in an estuarine, intertidal soft-sediment environment, Marine Ecology Progress Series, vol.244, pp.105-124, 2002.
DOI : 10.3354/meps244105

N. Alexandridis, C. Bacher, N. Desroy, and F. Jean, Building functional groups of marine benthic macroinvertebrates on the basis of general community assembly mechanisms, Journal of Sea Research, vol.121, pp.59-70, 2017.
DOI : 10.1016/j.seares.2017.01.007

URL : https://hal.archives-ouvertes.fr/hal-01510353

V. Campbell, P. Legendre, and F. Lapointe, Assessing Congruence Among Ultrametric Distance Matrices, Journal of Classification, vol.37, issue.1, pp.103-117, 2009.
DOI : 10.2307/2408332

J. M. Dambacher and P. A. Rossignol, The golden rule of complementary feedback, ACM SIGSAM Bulletin, vol.35, issue.4, pp.1-9, 2001.
DOI : 10.1145/509520.509522

J. M. Dambacher, H. W. Li, and P. A. Rossignol, RELEVANCE OF COMMUNITY STRUCTURE IN ASSESSING INDETERMINACY OF ECOLOGICAL PREDICTIONS, Ecology, vol.83, issue.5, pp.1372-1385, 2002.
DOI : 10.2307/1940449

J. M. Dambacher, H. W. Li, and P. A. Rossignol, Qualitative predictions in model ecosystems, Ecological Modelling, vol.161, issue.1-2, pp.79-93, 2003.
DOI : 10.1016/S0304-3800(02)00295-8

J. M. Dambacher and R. Ramos-jiliberto, UNDERSTANDING AND PREDICTING EFFECTS OF MODIFIED INTERACTIONS THROUGH A QUALITATIVE ANALYSIS OF COMMUNITY STRUCTURE, The Quarterly Review of Biology, vol.82, issue.3, pp.227-250, 2007.
DOI : 10.1086/519966

N. Desroy, Les peuplements benthiques de substrats meubles du bassin maritime de la Rance Évolution de la biodiversité et effets de l'activité prédatrice de Nephtys hombergii (Annélide Polychète) PhD Dissertation, 1998.

J. P. Grime, Benefits of plant diversity to ecosystems: immediate, filter and founder effects, Journal of Ecology, vol.51, issue.6, pp.902-910, 1998.
DOI : 10.1016/0169-5347(92)90006-W

B. Hérault, Reconciling niche and neutrality through the Emergent Group approach, Perspectives in Plant Ecology, Evolution and Systematics, vol.9, issue.2, pp.71-78, 2007.
DOI : 10.1016/j.ppees.2007.08.001

R. Kirby and C. Retière, Comparing environmental effects of Rance and Severn barrages, Proceedings of the Institution of Civil Engineers - Maritime Engineering, vol.162, issue.1, pp.11-26, 2009.
DOI : 10.1680/maen.2009.162.1.11

R. Levins, Qualitative mathematics for understanding, prediction, and intervention in complex ecosystems, Ecosyst Health, pp.178-204, 1998.

M. P. Marzloff, J. M. Dambacher, C. R. Johnson, L. R. Little, and S. D. Frusher, Exploring alternative states in ecological systems with a qualitative analysis of community feedback, Ecological Modelling, vol.222, issue.15, pp.2651-2662, 2011.
DOI : 10.1016/j.ecolmodel.2011.03.040