G. R. Almany, S. R. Connolly, D. D. Heath, J. D. Hogan, G. P. Jones et al., Connectivity, biodiversity conservation and the design of marine reserve networks for coral reefs, Coral Reefs, vol.42, issue.2, pp.339-351, 2009.
DOI : 10.1007/s00338-009-0484-x

E. Barrow, F. Mahler, L. Mosele, C. Mvoyi, and L. Ntahuga, Sound natural resource management: The foundation for achieving the MDGs in Somalia, 2007.

N. J. Bennett and P. Dearden, From measuring outcomes to providing inputs: Governance, management, and local development for more effective marine protected areas, Marine Policy, vol.50, pp.96-110, 2014.
DOI : 10.1016/j.marpol.2014.05.005

L. Berline, A. Rammou, A. Doglioli, A. Molcard, and A. Petrenko, A Connectivity-Based Eco-Regionalization Method of the Mediterranean Sea, PLoS ONE, vol.23, issue.7, 2014.
DOI : 10.1371/journal.pone.0111978.s002

URL : https://hal.archives-ouvertes.fr/hal-01242826

R. Billé and J. Rochette, Feasibility Assessment of an ICZM Protocol to the Nairobi Convention, 2010.

U. Bodenhofer, A. Kothmeier, and S. Hochreiter, APCluster: an R package for affinity propagation clustering, Bioinformatics, vol.27, issue.17, pp.2463-2464, 2011.
DOI : 10.1093/bioinformatics/btr406

S. P. Borgatti, Centrality and network flow, Social Networks, vol.27, issue.1, pp.55-71, 2005.
DOI : 10.1016/j.socnet.2004.11.008

A. Borja, S. B. Bricker, D. M. Dauer, N. T. Demetriades, J. G. Ferreira et al., Overview of integrative tools and methods in assessing ecological integrity in estuarine and coastal systems worldwide, Marine Pollution Bulletin, vol.56, issue.9, pp.1519-1537, 2008.
DOI : 10.1016/j.marpolbul.2008.07.005

L. W. Botsford, J. W. White, M. Coffroth, C. B. Paris, S. Planes et al., Connectivity and resilience of coral reef metapopulations in marine protected areas: matching empirical efforts to predictive needs, Coral Reefs, vol.46, issue.6, pp.327-337, 2009.
DOI : 10.1007/s00338-009-0466-z

URL : https://hal.archives-ouvertes.fr/halsde-00431816

J. Bourjea, Structure et connectivité de la mégafaune marine à l'échelle d'une région océanique: enjeux pour la gestion durable des tortues marines dans l'océan Indien occidental, Thèse de doctorat), p.169, 2014.

J. Bourjea, S. Lapègue, L. Gagnevin, D. Broderick, J. A. Mortimer et al., Phylogeography of the green turtle, Chelonia mydas, in the Southwest Indian Ocean, Molecular Ecology, vol.15, issue.1, pp.175-186, 2007.
DOI : 10.1111/j.1365-294X.2006.03122.x

P. Chapman, S. F. Marco, R. Davis, and A. Coward, Flow at intermediate depths around Madagascar based on ALACE float trajectories, Deep Sea Research Part II: Topical Studies in Oceanography, vol.50, issue.12-13, pp.1957-1986, 2003.
DOI : 10.1016/S0967-0645(03)00040-7

M. J. Costello, Long live Marine Reserves: A review of experiences and benefits, Biological Conservation, vol.176, pp.289-296, 2014.
DOI : 10.1016/j.biocon.2014.04.023

R. Cowen, G. Gawarkiewicz, J. Pineda, S. Thorrold, and F. Werner, Population Connectivity in Marine Systems: An Overview, Oceanography, vol.20, issue.3, pp.14-21, 2007.
DOI : 10.5670/oceanog.2007.26

R. K. Cowen, K. M. Lwiza, S. Sponaugle, C. B. Paris, and D. B. Olson, Connectivity of Marine Populations: Open or Closed?, Science, vol.287, issue.5454, 2000.
DOI : 10.1126/science.287.5454.857

R. K. Cowen and S. Sponaugle, Larval Dispersal and Marine Population Connectivity, Annual Review of Marine Science, vol.1, issue.1, pp.443-466, 2009.
DOI : 10.1146/annurev.marine.010908.163757

E. Crochelet, P. Chabanet, K. Pothin, E. Lagabrielle, J. Roberts et al., Validation of a fish larvae dispersal model with otolith data in the Western Indian Ocean and implications for marine spatial planning in data-poor regions, Ocean & Coastal Management, vol.86, pp.13-21, 2013.
DOI : 10.1016/j.ocecoaman.2013.10.002

URL : https://hal.archives-ouvertes.fr/hal-01239631

G. Csardi and T. Nepusz, The igraph software package for complex network research, Int. J. Complex Syst, p.1695, 2006.

P. B. Fenberg, J. E. Caselle, J. Claudet, M. Clemence, S. D. Gaines et al., The science of European marine reserves: Status, efficacy, and future needs, Marine Policy, vol.36, issue.5, pp.1012-1021, 2012.
DOI : 10.1016/j.marpol.2012.02.021

URL : https://hal.archives-ouvertes.fr/hal-00722776

M. M. Foley, B. S. Halpern, F. Micheli, M. H. Armsby, M. R. Caldwell et al., Guiding ecological principles for marine spatial planning, Marine Policy, vol.34, issue.5, pp.955-966, 2010.
DOI : 10.1016/j.marpol.2010.02.001

B. J. Frey and D. Dueck, Clustering by Passing Messages Between Data Points, Science, vol.315, issue.5814, pp.972-976, 2007.
DOI : 10.1126/science.1136800

S. D. Gaines, C. White, M. H. Carr, and S. R. Palumbi, Designing marine reserve networks for both conservation and fisheries management, Proc. Natl. Acad, 2010.
DOI : 10.1073/pnas.0906473107

S. M. Garcia, H. Cohen, D. Freestone, C. Martinez, N. Oral et al., An Ecosystem Approach to Management of Seamounts in the Southern Indian Ocean, ? A Road Map Towards Sustainable use and Conservation of Biodiversity in the Southern Indian Ocean. IUCN, Gland, Switzerland, p.32, 2013.

J. A. García-charton, A. Pérez-ruzafa, C. Marcos, J. Claudet, F. Badalamenti et al., Effectiveness of European Atlanto-Mediterranean MPAs: Do they accomplish the expected effects on populations, communities and ecosystems?, Journal for Nature Conservation, vol.16, issue.4, pp.193-221, 2008.
DOI : 10.1016/j.jnc.2008.09.007

T. A. Gardner, I. M. Côté, J. A. Gill, A. Grant, and A. R. Watkinson, HURRICANES AND CARIBBEAN CORAL REEFS: IMPACTS, RECOVERY PATTERNS, AND ROLE IN LONG-TERM DECLINE, Ecology, vol.86, issue.1, pp.174-184, 2005.
DOI : 10.1126/science.214.4522.749

I. Ginis, Tropical Cyclone-Ocean Interactions. Atmosphere-Ocean Interactions, Advances in Fluid Mechanics Series, pp.83-114, 2002.

H. Gjertsen, Can Habitat Protection Lead to Improvements in Human Well-Being? Evidence from Marine Protected Areas in the Philippines, World Development, vol.33, issue.2, pp.199-217, 2005.
DOI : 10.1016/j.worlddev.2004.07.009

N. J. Gray, Producing Success: Co-Management of a Marine Protected Area in Belize. (unpublished paper), 2008.

A. L. Green, L. Fernandes, G. Almany, R. Abesamis, E. Mcleod et al., Designing Marine Reserves for Fisheries Management, Biodiversity Conservation, and Climate Change Adaptation, Coastal Management, vol.42, issue.2, pp.143-159, 2014.
DOI : 10.1080/08920753.2014.878177

URL : https://hal.archives-ouvertes.fr/hal-01333534

J. Guerreiro, A. Chircop, C. Grilo, A. Viras, R. Ribeiro et al., Establishing a transboundary network of marine protected areas: Diplomatic and management options for the east African context, Marine Policy, vol.34, issue.5, pp.896-910, 2010.
DOI : 10.1016/j.marpol.2010.01.014

P. Guidetti, M. Milazzo, S. Bussotti, A. Molinari, M. Murenu et al., Italian marine reserve effectiveness: Does enforcement matter?, Biological Conservation, vol.141, issue.3, pp.699-709, 2008.
DOI : 10.1016/j.biocon.2007.12.013

B. S. Halpern, S. Walbridge, K. A. Selkoe, C. V. Kappel, F. Micheli et al., A Global Map of Human Impact on Marine Ecosystems, Science, vol.319, issue.5865, pp.948-952, 2009.
DOI : 10.1126/science.1149345

M. L. Harmelin-vivien, The effects of storms and cyclones on coral reefs: a review, J. Coast. Res, pp.211-231, 1994.

T. B. Hoareau, E. Boissin, G. Paulay, and J. H. Bruggemann, The Southwestern Indian Ocean as a potential marine evolutionary hotspot: perspectives from comparative phylogeography of reef brittle-stars, Journal of Biogeography, vol.6, issue.11, pp.2167-2179, 2013.
DOI : 10.1111/jbi.12155

URL : https://hal.archives-ouvertes.fr/hal-01369697

O. Hoegh-guldberg, P. J. Mumby, A. J. Hooten, R. S. Steneck, P. Greenfield et al., Coral Reefs Under Rapid Climate Change and Ocean Acidification, Science, vol.318, issue.5857, pp.1737-1742, 2007.
DOI : 10.1126/science.1152509

T. P. Hughes, A. H. Baird, D. R. Bellwood, M. Card, S. R. Connolly et al., Climate Change, Human Impacts, and the Resilience of Coral Reefs, Science, vol.301, issue.5635, pp.929-933, 2003.
DOI : 10.1126/science.1085046

M. N. Jacobi, C. André, K. Döös, and P. R. Jonsson, Identification of subpopulations from connectivity matrices, Ecography, vol.20, issue.11, pp.1004-1016, 2012.
DOI : 10.1111/j.1600-0587.2012.07281.x

G. P. Jones, G. R. Russ, P. F. Sale, and R. S. Steneck, Theme section on ???Larval connectivity, resilience and the future of coral reefs???, Coral Reefs, vol.20, issue.2, pp.303-305, 2009.
DOI : 10.1007/s00338-008-0440-1

G. Jones, M. Srinivasan, and G. Almany, Population Connectivity and Conservation of Marine Biodiversity, Oceanography, vol.20, issue.3, pp.100-111, 2007.
DOI : 10.5670/oceanog.2007.33

M. J. Kingsford, J. M. Leis, A. Shanks, K. C. Lindeman, S. G. Morgan et al., Sensory environments, larval abilities and local self-recruitment, Bull. Mar. Sci, vol.70, pp.309-340, 2002.

S. Kininmonth, G. De-'ath, and H. Possingham, Graph theoretic topology of the Great but small Barrier Reef world, Theoretical Ecology, vol.393, issue.2, pp.75-88, 2010.
DOI : 10.1007/s12080-009-0055-3

D. D. Laffoley, Towards Networks of Marine Protected Areas. The MPA Plan of Action for IUCN's World Commission on Protected Areas, pp.978-980, 2008.

J. M. Leis, Larval fish dispersal and the east Pacific barrier, Océanogr. Trop, vol.19, pp.181-192, 1984.

J. Leis, Pacific coral-reef fishes: The implications of behaviour and ecology of larvae for biodiversity and conservation, and a reassessment of the open population paradigm, Environmental Biology of Fishes, vol.65, issue.2, pp.199-208, 2002.
DOI : 10.1023/A:1020096720543

S. Lester, B. Halpern, K. Grorud-colvert, J. Lubchenco, B. Ruttenberg et al., Biological effects within no-take marine reserves: a global synthesis, Marine Ecology Progress Series, vol.384, pp.33-46, 2009.
DOI : 10.3354/meps08029

J. R. Lutjeharms and T. G. Bornman, The importance of the greater Agulhas Current is increasingly being recognised. South Afr, J. Sci, vol.106, p.160, 2010.

L. J. Mccook, G. R. Almany, M. L. Berumen, J. C. Day, A. L. Green et al., Management under uncertainty: guide-lines for incorporating connectivity into the protection of coral reefs, Coral Reefs, vol.17, issue.2, pp.353-366, 2009.
DOI : 10.1007/s00338-008-0463-7

URL : https://hal.archives-ouvertes.fr/halsde-00459263

E. Mcleod, R. Salm, A. Green, and J. Almany, Designing marine protected area networks to address the impacts of climate change, Frontiers in Ecology and the Environment, vol.11, issue.7, pp.362-370, 2008.
DOI : 10.1007/s00338-003-0361-y

F. Moberg and C. Folke, Ecological goods and services of coral reef ecosystems, Ecological Economics, vol.29, issue.2, pp.215-233, 1999.
DOI : 10.1016/S0921-8009(99)00009-9

D. Moffat, M. Ngoile, O. Linden, and J. Francis, The reality of the stomach: coastal management at the local level in Eastern Africa, Ambio, vol.27, pp.590-598, 1998.

C. Mora, E. A. Treml, J. Roberts, K. Crosby, D. Roy et al., High connectivity among habitats precludes the relationship between dispersal and range size in tropical reef fishes, Ecography, vol.230, issue.1, pp.89-96, 2012.
DOI : 10.1111/j.1600-0587.2011.06874.x

D. Mouillot, J. M. Culioli, D. Pelletier, and J. A. Tomasini, Do we protect biological originality in protected areas? A new index and an application to the Bonifacio Strait Natural Reserve, Biological Conservation, vol.141, issue.6, pp.1569-1580, 2008.
DOI : 10.1016/j.biocon.2008.04.002

D. Muths, G. Gouws, M. Mwale, E. Tessier, J. Bourjea et al., at the scale of the western Indian Ocean, Canadian Journal of Fisheries and Aquatic Sciences, vol.69, issue.5, pp.842-853, 2012.
DOI : 10.1139/f2012-012

D. Muths, E. Tessier, and J. Bourjea, in the West Indian Ocean appears congruent with biogeographic and oceanographic boundaries, Marine Ecology, vol.292, issue.13, pp.447-461, 2015.
DOI : 10.1111/maec.12153

D. Muths, E. Tessier, G. Gouws, M. Craig, M. Mwale et al., Restricted dispersal of the reef fish Myripristis berndti at the scale of the SW Indian Ocean, Marine Ecology Progress Series, vol.443, pp.167-180, 2011.
DOI : 10.3354/meps09394

D. Obura, The diversity and biogeography of Western Indian ocean reefbuilding corals, PLoS One, vol.7, 2012.

D. Obura, J. Church, C. Daniels, H. Kalombo, M. Shleyer et al., Status of coral reefs in East Africa, 2004.

S. Planes, G. P. Jones, and S. R. Thorrold, Larval dispersal connects fish populations in a network of marine protected areas, Proc. Natl. Acad. Sci, pp.5693-5697, 2009.
DOI : 10.1073/pnas.0808007106

URL : https://hal.archives-ouvertes.fr/halsde-00431334

J. M. Pujolar, M. Schiavina, D. Franco, A. Melià, P. Guidetti et al., Understanding the effectiveness of marine protected areas using genetic connectivity patterns and Lagrangian simulations, Diversity and Distributions, vol.11, issue.301, pp.1531-1542, 2013.
DOI : 10.1111/ddi.12114

R. Team, R: a language and environment for statistical computing. R Foundation for Statistical Computing, 2012.

C. M. Roberts, Connectivity and Management of Caribbean Coral Reefs, Science, vol.278, issue.5342, pp.1454-1457, 1997.
DOI : 10.1126/science.278.5342.1454

J. J. Roberts, B. D. Best, D. C. Dunn, E. A. Treml, and P. N. Halpin, Marine Geospatial Ecology Tools: An integrated framework for ecological geoprocessing with ArcGIS, Python, R, MATLAB, and C++, Environmental Modelling & Software, vol.25, issue.10, pp.1197-1207, 2010.
DOI : 10.1016/j.envsoft.2010.03.029

C. M. Roberts, J. P. Hawkins, J. Fletcher, S. Hands, K. Raab et al., Guidance on the size and spacing of marine protected areas in England, 2010.

S. Rocliffe, S. Peabody, M. Samoilys, and J. P. Hawkins, Towards A Network of Locally Managed Marine Areas (LMMAs) in the Western Indian Ocean, PLoS ONE, vol.44, issue.7, 2014.
DOI : 10.1371/journal.pone.0103000.s002

V. Rossi, E. Ser-giacomi, C. López, and E. Hernández-garcía, Hydrodynamic provinces and oceanic connectivity from a transport network help designing marine reserves, Geophysical Research Letters, vol.40, issue.4, pp.2883-2891, 2014.
DOI : 10.1029/2012GL054519

J. S. Rossiter and A. Levine, What makes a ???successful??? marine protected area? The unique context of Hawaii???s fish replenishment areas, Marine Policy, vol.44, pp.196-203, 2014.
DOI : 10.1016/j.marpol.2013.08.022

G. R. Russ, A. C. Alcala, A. P. Maypa, H. P. Calumpong, and A. T. White, MARINE RESERVE BENEFITS LOCAL FISHERIES, Ecological Applications, vol.14, issue.2, pp.597-606, 2004.
DOI : 10.1139/cjfas-55-4-917

P. F. Sale, R. K. Cowen, B. S. Danilowicz, G. P. Jones, J. P. Kritzer et al., Critical science gaps impede use of no-take fishery reserves, Trends in Ecology & Evolution, vol.20, issue.2, pp.74-80, 2005.
DOI : 10.1016/j.tree.2004.11.007

R. V. Salm and S. L. Coles, Coral bleaching and marine protected areas Proceedings of the workshop on mitigating coral bleaching impact through MPA design. Asia Pacific coastal marine program Report #0102, Bishop Museum, pp.29-31, 2001.

E. T. Schultz and R. K. Cowen, Recruitment of coral-reef fishes to Bermuda: local retention or long-distance transport?, Marine Ecology Progress Series, vol.109, pp.15-28, 1994.
DOI : 10.3354/meps109015

M. D. Spalding, I. Meliane, A. Milam, C. Fitzgerald, and L. Z. Hale, Protecting Marine Spaces: Global Targets and Changing Approaches, Ocean Yearbook Online, vol.27, issue.1, pp.213-248, 2013.
DOI : 10.1163/22116001-90000160

U. T. Srinivasan, R. Watson, and U. Rashid-sumaila, Global fisheries losses at the exclusive economic zone level, 1950 to present, Marine Policy, vol.36, issue.2, pp.544-549, 2012.
DOI : 10.1016/j.marpol.2011.10.001

Y. Tessema and R. V. Salm, Kenya Wildlife Service IUCN Eastern Africa Programme IUCN East Africa Regional Office. Partnership for conservation: report of the Regional Workshop on Marine Protected Areas, Tourism, and Communities, pp.11-13, 1998.

M. Tomczak and J. S. Godfrey, Regional Oceanography: An Introduction, second ed, p.390, 2003.

C. Toropova, I. Meliane, D. Laffoley, E. Matthews, and M. Spalding, Global Ocean Protection Present Status and Future Possibilities Agence des aires marines protégées, IUCN WCPA, p.96, 2010.

E. A. Treml, P. N. Halpin, D. L. Urban, and L. F. Pratson, Modeling population connectivity by ocean currents, a graph-theoretic approach for marine conservation, Landscape Ecology, vol.9, issue.S1, pp.19-36, 2008.
DOI : 10.1007/s10980-007-9138-y

E. A. Treml, J. J. Roberts, Y. Chao, P. N. Halpin, H. P. Possingham et al., Reproductive Output and Duration of the Pelagic Larval Stage Determine Seascape-Wide Connectivity of Marine Populations, Integrative and Comparative Biology, vol.52, issue.4, pp.525-537, 2012.
DOI : 10.1093/icb/ics101

B. C. Victor, Growth, dispersal, and identification of planktonic labrid and pomacentrid reef-fish larvae in the eastern Pacific Ocean, Marine Biology, vol.3, issue.3, pp.145-152, 1987.
DOI : 10.1007/BF00447496

P. Wessel and W. H. Smith, A global, self-consistent, hierarchical, high-resolution shoreline database, Journal of Geophysical Research: Solid Earth, vol.76, issue.33, pp.8741-8743, 1978.
DOI : 10.1029/96JB00104

C. Wilkinson, Status of coral reefs of the world: 2008. Global Coral Reef Monitoring Network and Reef and Rainforest Research Centre, 2008.

S. K. Wilson, M. Adjeroud, D. R. Bellwood, M. L. Berumen, D. Booth et al., Crucial knowledge gaps in current understanding of climate change impacts on coral reef fishes, Journal of Experimental Biology, vol.213, issue.6, pp.894-900, 2010.
DOI : 10.1242/jeb.037895