N. Juan-de, Glorieuses) were collected during the TAAF /INEE-sponsored PHYLIP expedition Field work was done under Surat Izin Penelitihan no, OD no OD no, 2007.

F. , C. Ird, L. , T. Arakaki, R. Beldade et al., the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank S, Province Sud. Fish sampling at Iles Eparses was authorized under Arrêté no. 2011-32 of Terres australes et antarctiques françaises Yang for help in sampling in the Red Sea, Iles Eparses, Madagascar, the South China Sea, the Philippines, West Papua, New Caledonia, and the Society Islands. We would like to thank L. Sorenson and B. Frédérich for assisting in English proofreading and for comments on the manuscript

G. Allen, Conservation hotspots of biodiversity and endemism for Indo-Pacific coral reef fishes Aquatic Conservation: Marine and Freshwater Ecosystems, pp.541-556, 2008.

J. Avise, Molecular Markers Sinauer, Natural History, and Evolution, issue.2, 2004.

H. Bandelt, P. Forster, and A. Röhl, Median-joining networks for inferring intraspecific phylogenies, Molecular Biology and Evolution, vol.16, issue.1, pp.37-48, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026036

F. Bonjean and G. Lagerloef, Diagnostic Model and Analysis of the Surface Currents in the Tropical Pacific Ocean, Journal of Physical Oceanography, vol.32, issue.10, pp.2938-2954, 2002.
DOI : 10.1175/1520-0485(2002)032<2938:DMAAOT>2.0.CO;2

C. Boender, R. Kan, and A. , Bayesian stopping rules for multistart global optimization methods, Mathematical Programming, vol.21, issue.1981, pp.59-80, 1987.
DOI : 10.1007/BF02591684

B. Bowen, L. Rocha, R. Toonen, S. Karl, T. The et al., The origins of tropical marine biodiversity, Trends in Ecology & Evolution, vol.28, issue.6, pp.359-366, 2013.
DOI : 10.1016/j.tree.2013.01.018

J. Briggs, Marine zoogeography, 1974.

J. Briggs, Extinction and replacement in the Indo-West Pacific Ocean, Journal of Biogeography, vol.19, issue.4, pp.777-783, 1999.
DOI : 10.1007/s003380050241

P. Buston, C. Fauvelot, M. Wong, and S. Planes, : small, similar-sized individuals may be close kin, Molecular Ecology, vol.19, issue.22, pp.4707-4715, 2009.
DOI : 10.1111/j.1365-294X.2009.04383.x

M. Craig, J. Eble, B. Bowen, and D. Robertson, High genetic connectivity across the Indian and Pacific Oceans in the reef fish Myripristis berndti (Holocentridae), Marine Ecology Progress Series, vol.334, pp.245-254, 2007.
DOI : 10.3354/meps334245

D. Darriba, G. Taboada, R. Doallo, and D. Posada, jModelTest 2: more models, new heuristics and parallel computing, Nature Methods, vol.9, issue.8, p.772, 2012.
DOI : 10.1109/TAC.1974.1100705

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594756

J. Dibattista, M. Berumen, M. Gaither, L. Rocha, J. Eble et al., After continents divide: comparative phylogeography of reef fishes from the Red Sea and Indian Ocean, Journal of Biogeography, vol.66, issue.6, pp.1170-1181, 2013.
DOI : 10.1111/jbi.12068

J. Drew and P. Barber, Sequential cladogenesis of the reef fish Pomacentrus moluccensis (Pomacentridae) supports the peripheral origin of marine biodiversity in the Indo-Australian archipelago, Molecular Phylogenetics and Evolution, vol.53, issue.1, pp.335-339, 2009.
DOI : 10.1016/j.ympev.2009.04.014

J. Eble, L. Rocha, M. Craig, and B. Bowen, ), Journal of Marine Biology, vol.20, issue.2370, p.518516, 2011.
DOI : 10.1098/rspb.2003.2405

G. Evanno, S. Regnaut, and J. Goudet, Detecting the number of clusters of individuals using the software structure: a simulation study, Molecular Ecology, vol.16, issue.8, pp.2611-2620, 2005.
DOI : 10.1098/rspb.2001.1600

L. Excoffier, G. Laval, and S. Schneider, Arlequin ver. 3.0: an integrated software package for population genetics data analysis, Evolutionary Bioinformatics Online, vol.1, pp.47-50, 2005.

D. Falush, M. Stephens, and J. Pritchard, Inference of population structure using multilocus genotype data: dominant markers and null alleles, Molecular Ecology Notes, vol.298, issue.4, pp.574-578, 2007.
DOI : 10.1111/j.1471-8286.2007.01758.x

C. Fauvelot and P. Borsa, Patterns of genetic isolation in a widely distributed pelagic fish, the narrow-barred Spanish mackerel (Scomberomorus commerson), Biological Journal of the Linnean Society, vol.104, issue.4, pp.886-902, 2011.
DOI : 10.1111/j.1095-8312.2011.01754.x

URL : https://hal.archives-ouvertes.fr/ird-00759711

C. Fauvelot and S. Planes, Understanding origins of present-day genetic structure in marine fish: biologically or historically driven patterns, Marine Biology, vol.141, pp.773-788, 2002.

C. Fauvelot, C. Smith-keune, D. Jerry, P. Buston, and S. Planes, Isolation and characterization of 16 microsatellite loci in the humbug damselfish, Dascyllus aruanus (family Pomacentridae), Molecular Ecology Resources, vol.6, issue.2, pp.651-653, 2009.
DOI : 10.1111/j.1755-0998.2008.02500.x

URL : https://hal.archives-ouvertes.fr/halsde-00459187

M. Gaither, B. Bowen, T. Bordenave, L. Rocha, S. Newman et al., Phylogeography of the reef fish Cephalopholis argus(Epinephelidae) indicates Pleistocene isolation across the indo-pacific barrier with contemporary overlap in the coral triangle, BMC Evolutionary Biology, vol.412, issue.5, p.189, 2011.
DOI : 10.1186/1471-2148-11-189

M. Gaither, S. Jones, C. Kelley, S. Newman, L. Sorenson et al., High Connectivity in the Deepwater Snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with Isolation of the Hawaiian Archipelago, High connectivity in the deepwater snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with isolation of the Hawaiian archipelago, p.28913, 2011.
DOI : 10.1371/journal.pone.0028913.t005

M. Gaither and L. Rocha, Origins of species richness in the Indo-Malay-Philippine biodiversity hotspot: evidence for the centre of overlap hypothesis, Journal of Biogeography, vol.33, issue.9, pp.1638-1648, 2013.
DOI : 10.1111/jbi.12126

M. Gaither, R. Toonen, D. Robertson, S. Planes, and B. Bowen, Genetic evaluation of marine biogeographical barriers: perspectives from two widespread Indo-Pacific snappers (Lutjanus kasmira and Lutjanus fulvus), Journal of Biogeography, vol.230, issue.1, pp.133-147, 2010.
DOI : 10.1111/j.1365-2699.2009.02188.x

URL : https://hal.archives-ouvertes.fr/hal-00609442

J. Goudet, FSTAT, a program to estimate and test gene diversities and fixation indices (v Available from: www2, 2001.

W. Grant and B. Bowen, Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation, Journal of Heredity, vol.89, issue.5, pp.415-426, 1998.
DOI : 10.1093/jhered/89.5.415

R. Harpending, Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution, Human Biology, vol.66, pp.591-600, 1994.

S. Holbrook, G. Forrester, and R. Schmitt, Spatial patterns in abundance of a damselfish reflect availability of suitable habitat, Oecologia, vol.122, issue.1, pp.109-120, 2000.
DOI : 10.1007/PL00008826

J. Horne, L. Van-herwerden, J. Choat, and D. Robertson, High population connectivity across the Indo-Pacific: Congruent lack of phylogeographic structure in three reef fish congeners, Molecular Phylogenetics and Evolution, vol.49, issue.2, pp.629-638, 2008.
DOI : 10.1016/j.ympev.2008.08.023

J. Huelsenbeck and F. Ronquist, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, vol.17, issue.8, pp.754-755, 2001.
DOI : 10.1093/bioinformatics/17.8.754

J. Jensen, A. Bohonak, and S. Kelley, Isolation by distance, web service, BMC Genetics, vol.6, issue.1, p.13, 2005.
DOI : 10.1186/1471-2156-6-13

K. Johannesson and C. Andre, Life on the margin: genetic isolation and diversity loss in a peripheral marine ecosystem, the Baltic Sea, Molecular Ecology, vol.325, issue.8, pp.2013-2029, 2006.
DOI : 10.1111/j.1365-294X.2006.02919.x

P. Sale, Apparent effect of prior experience on a habitat preference exhibited by the reef fish, Dascyllus aruanus (Pisces: Pomacentridae), Animal Behaviour, vol.19, issue.2, pp.251-256, 1971.
DOI : 10.1016/S0003-3472(71)80005-2

P. Sale, Extremely Limited Home Range in a Coral Reef Fish, Dascyllus aruanus (Pisces; Pomacentridae), Copeia, vol.1971, issue.2, pp.324-327, 1971.
DOI : 10.2307/1442839

P. Sale, Influence of Corals in the Dispersion of the Pomacentrid Fish, Dascyllus Aruanus, Ecology, vol.53, issue.4, pp.741-744, 1972.
DOI : 10.2307/1934795

M. Siddall, E. Rohling, A. Almogi-labin, C. Hemleben, D. Meischner et al., Sea-level fluctuations during the last glacial cycle, Nature, vol.423, issue.6942, pp.853-858, 2003.
DOI : 10.1038/nature01690

R. Sokal and F. Rohlf, Biometry, The Principles and Practice of, Statistics in Biological Research, vol.3, 1995.

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006.
DOI : 10.1093/bioinformatics/btl446

H. Sweatman, The Influence of Adults of Some Coral Reef Fishes on Larval Recruitment, Ecological Monographs, vol.55, issue.4, pp.469-485, 1985.
DOI : 10.2307/2937132

H. Sweatman, Field evidence that settling coral reef fish larvae detect resident fishes using dissolved chemical cues, Journal of Experimental Marine Biology and Ecology, vol.124, issue.3, pp.163-174, 1988.
DOI : 10.1016/0022-0981(88)90170-0

L. Van-herwerden, J. Choat, S. Newman, M. Leray, and G. Hillersøy, Complex patterns of population structure and recruitment of Plectropomus leopardus (Pisces: Epinephelidae) in the Indo-West Pacific: implications for fisheries management, Marine Biology, vol.52, issue.1, pp.1595-1607, 2009.
DOI : 10.1007/s00227-009-1195-0

C. Van-oosterhout, W. Hutchinson, D. Wills, and P. Shipley, micro-checker: software for identifying and correcting genotyping errors in microsatellite data, Molecular Ecology Notes, vol.8, issue.3, pp.535-538, 2004.
DOI : 10.1046/j.1365-294x.1998.00477.x

H. Voris, Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations, Journal of Biogeography, vol.313, issue.5, pp.1153-1167, 2000.
DOI : 10.1016/0277-3791(87)90003-5

B. Weir and C. Cockerham, Estimating F-Statistics for the Analysis of Population Structure, Evolution, vol.38, issue.6, pp.1358-1370, 1984.
DOI : 10.2307/2408641

G. Wellington and B. Victor, Planktonic larval duration of one hundred species of Pacific and Atlantic damselfishes (Pomacentridae), Marine Biology, vol.30, issue.4, pp.557-567, 1989.
DOI : 10.1007/BF00541659

K. Winters, L. Van-herwerden, J. Choat, and D. Robertson, Phylogeography of the Indo-Pacific parrotfish Scarus psittacus: isolation generates distinctive peripheral populations in two oceans, Marine Biology, vol.96, issue.8, pp.1679-1691, 2010.
DOI : 10.1007/s00227-010-1442-4