A. Appendix, GENBANK accession numbers for D. abudafur / D. aruanus were KF754733-KF754795 and 6 additional cytochrome b gene sequences from Madang (GENBANK nos KT258989-KT258994); those for E. areolatus were DQ107866-DQ107870 NC_020785; those for E. fasciatus were DQ107873-DQ107876, Database accession numbers for nucleotide sequences CRYOBANK accession number for E. fasciatus was ASIZP0800173 KJ202153-KJ202155 and KJ594972- KJ594972, and an additional CO1 gene sequences from Glorieuses Islands, pp.130967-130969

B. Appendix, S. G. Alcantara, and A. V. Yambot, Supplementary data Supplementary data related to this article can be DNA barcoding of commercially important grouper species (Perciformes, Serranidae) in the Philippines, p.958672, 2014.

G. R. Allen, Conservation hotspots of biodiversity and endemism for Indo-Pacific coral reef fishes, Aquatic Conservation: Marine and Freshwater Ecosystems, vol.1, issue.3, pp.541-556, 2008.
DOI : 10.1002/aqc.880

G. R. Allen and M. V. Erdmann, Reef fishes of the East Indies, vols. I-III, Tropical Reef Research, 2012.

I. S. Arlyza, K. Shen, J. Durand, and P. Borsa, Mitochondrial Haplotypes Indicate Parapatric-like Phylogeographic Structure in Blue-Spotted Maskray (Neotrygon kuhlii) from the Coral Triangle Region, Journal of Heredity, vol.104, issue.5, pp.725-733, 2013.
DOI : 10.1093/jhered/est044
URL : https://hal.archives-ouvertes.fr/ird-00853606

H. Asgharian, H. H. Sahafi, A. A. Ardalan, S. Shekarriz, and E. Elahi, Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species, Molecular Ecology Resources, vol.9, issue.Suppl. 1, pp.461-472, 2011.
DOI : 10.1111/j.1755-0998.2011.02989.x

J. C. Avise, Phylogeography: the history and formation of species, 2000.

H. J. 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

R. Beldade, S. J. Holbrook, R. J. Schmitt, S. Planes, D. Malone et al., Larger female fish contribute disproportionately more to self-replenishment, Proceedings of the Royal Society B: Biological Sciences, vol.52, issue.12, pp.2116-2121, 2012.
DOI : 10.1371/journal.pone.0015715
URL : https://hal.archives-ouvertes.fr/hal-00722765

D. R. Bellwood, T. P. Hughes, S. R. Connolly, and J. Tanner, Environmental and geometric constraints on Indo-Pacific coral reef biodiversity, Ecology Letters, vol.72, issue.6, 2005.
DOI : 10.1111/j.1461-0248.2005.00763.x

D. R. Bellwood, W. Renema, and B. R. Rosen, Biodiversity hotspots, evolution and coral reef biogeography, pp.216-245, 2012.
DOI : 10.1017/CBO9780511735882.011

E. Bermingham and C. Moritz, Comparative phylogeography: concepts and applications, Molecular Ecology, vol.7, issue.4, pp.367-369, 1998.
DOI : 10.1046/j.1365-294x.1998.00308.x

P. Borsa, I. S. Arlyza, W. Chen, J. Durand, M. G. Meekan et al., Resurrection of New Caledonian maskray Neotrygon trigonoides (Myliobatoidei: Dasyatidae) from synonymy with N.??kuhlii, based on cytochrome-oxidase I gene sequences and spotting patterns, Comptes Rendus Biologies, vol.336, issue.4, pp.221-232, 2013.
DOI : 10.1016/j.crvi.2013.05.005
URL : https://hal.archives-ouvertes.fr/ird-00847459

P. Borsa, D. Hsiao, K. E. Carpenter, and W. Chen, Cranial morphometrics and mitochondrial DNA sequences distinguish cryptic species of the longface emperor (Lethrinus olivaceus), an emblematic fish of Indo-West Pacific coral reefs, Comptes Rendus Biologies, vol.336, issue.10, pp.505-514, 2013.
DOI : 10.1016/j.crvi.2013.09.004
URL : https://hal.archives-ouvertes.fr/ird-00915470

P. Borsa, A. Sembiring, C. Fauvelot, and W. Chen, Resurrection of Indian Ocean humbug damselfish, Dascyllus abudafur (Forssk??l) from synonymy with its Pacific Ocean sibling, Dascyllus aruanus (L.), Comptes Rendus Biologies, vol.337, issue.12, pp.709-716, 2014.
DOI : 10.1016/j.crvi.2014.09.001

J. C. Briggs, Marine centres of origin as evolutionary engines, Journal of Biogeography, vol.32, issue.Suppl., pp.1-18, 2003.
DOI : 10.1046/j.1365-2699.2003.00810.x

J. C. Briggs, B. W. Bowen, K. E. Carpenter, P. H. Barber, E. D. Crandall et al., A realignment of marine biogeographic provinces with particular reference to fish distributions, Journal of Biogeography, vol.292, issue.Suppl. 2, pp.12-30, 2011.
DOI : 10.1111/j.1365-2699.2011.02613.x

J. Cracraft and R. O. Prum, Patterns and Processes of Diversification: Speciation and Historical Congruence in Some Neotropical Birds, Evolution, vol.42, issue.3, pp.603-620, 1988.
DOI : 10.2307/2409043

E. D. Crandall, M. A. Frey, R. K. Grosberg, and P. H. Barber, Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropods, Molecular Ecology, vol.42, issue.2, pp.611-626, 2008.
DOI : 10.1111/j.1365-294X.2007.03600.x

E. D. Crandall, E. A. Treml, L. Liggins, L. Gleeson, N. Yasuda et al., Return of the ghosts of dispersal past: historical spread and contemporary gene flow in the blue sea star <I>Linckia laevigata</I>, Bulletin of Marine Science, vol.90, issue.1, pp.399-425, 2014.
DOI : 10.5343/bms.2013.1052

E. E. Demartini and A. M. Friedlander, Spatial patterns of endemism in shallow-water reef fish populations of the Northwestern Hawaiian Islands, Marine Ecology Progress Series, vol.271, pp.281-296, 2004.
DOI : 10.3354/meps271281

J. D. Dibattista, L. A. Rocha, M. T. Craig, K. A. Feldheim, B. W. Bowen et al., Phylogeography of two closely related Indo-Pacific butterflyfishes reveals divergent evolutionary histories and discordant results from mtDNA and microsatellites Endemism and regional color and genetic differences in five putatively cosmopolitan reef fishes, J. Hered. Conserv. Biol, vol.103, issue.22, pp.617-629, 2008.

J. Durand and P. Borsa, Mitochondrial phylogeny of grey mullets (Acanthopterygii: Mugilidae) suggests high proportion of cryptic species, Comptes Rendus Biologies, vol.338, issue.4, 2015.
DOI : 10.1016/j.crvi.2015.01.007
URL : https://hal.archives-ouvertes.fr/ird-01144054

J. Durand, W. Chen, K. Shen, C. Fu, and P. Borsa, Genus-level taxonomic changes implied by the mitochondrial phylogeny of grey mullets (Teleostei: Mugilidae), Comptes Rendus Biologies, vol.335, issue.10-11, pp.687-697, 2012.
DOI : 10.1016/j.crvi.2012.09.005
URL : https://hal.archives-ouvertes.fr/ird-00759075

B. C. Emerson and R. G. Gillespie, Phylogenetic analysis of community assembly and structure over space and time, Trends in Ecology & Evolution, vol.23, issue.11, pp.519-530, 2008.
DOI : 10.1016/j.tree.2008.07.005

L. Excoffier and H. E. Lischer, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Molecular Ecology Resources, vol.127, issue.3, pp.564-567, 2010.
DOI : 10.1111/j.1755-0998.2010.02847.x

L. Excoffier, P. E. Smouse, and J. M. Quattro, Analysis of molecular variance inferred from metric distances among DNA haplotypes -Application to human mitochondrial-DNA restriction data, Genetics, vol.131, pp.479-491, 1992.

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

R. Froese and D. Pauly, FishBase, World Wide Web electronic publication, www.fishbase.org, version, 2013.

M. R. Gaither, B. W. Bowen, T. R. Bordenave, L. A. Rocha, S. J. 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, 2011.
DOI : 10.1186/1471-2148-11-189

M. R. Gaither and L. A. 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. R. Gaither, R. J. Toonen, D. R. Robertson, S. Planes, and B. W. 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. S. Goldstein, H. Matsuda, T. Takenouchi, and M. Butler, The complete development of larval Caribbean spiny lobster, Panulirus argus, in culture, J. J. Crustacean Biol, vol.4, issue.28, pp.306-327, 2008.

A. Griekspoor and T. Groothuis, 4PEAKS: a program that helps molecular biologists to visualize and edit their DNA sequence files, 2005.

T. A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program 20, 1999.

M. Hasegawa, H. Kishino, and T. Yano, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, Journal of Molecular Evolution, vol.275, issue.3, pp.160-74, 1985.
DOI : 10.1007/BF02101694

B. He, T. Lai, Z. Peng, X. Wang, and L. Pan, Complete mitogenome of the areolate grouper Epinephelus areolatus (Serranidae, Epinephelinae). Mitoch, DNA, vol.24, pp.498-500, 2013.

M. A. Hixon, D. W. Johnson, and S. M. Sogard, BOFFFFs: on the importance of conserving old-growth age structure in fishery populations, ICES Journal of Marine Science, vol.71, issue.8, pp.2171-2185, 2014.
DOI : 10.1093/icesjms/fst200

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

J. A. Hobbs, A. J. Frisch, G. R. Allen, and L. Van-herwerden, Marine hybrid hotspot at Indo-Pacific biogeographic border, Biology Letters, vol.26, issue.1, pp.258-261, 2009.
DOI : 10.1016/j.ympev.2006.02.012

J. A. Hobbs, S. J. Newman, G. E. Mitsopoulos, M. J. Travers, C. L. Skepper et al., Checklist and new records of Christmas Island fishes: the influence of isolation, biogeography and habitat availability on species abundance and community composition, Raffles B. Zool, vol.30, pp.184-202, 2014.

J. B. Horne, L. Van-herwerden, J. H. Choat, and D. R. 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

N. Hubert, V. Calcagno, R. S. Etienne, and N. Mouquet, Metacommunity speciation models and their implications for diversification theory, Ecology Letters, vol.158, issue.8, pp.864-881, 2015.
DOI : 10.1111/ele.12458

N. Hubert, F. Duponchelle, J. Nuñez-rodiguez, G. Davila, C. Paugy et al., Phylogeography of the piranha genera Serrasalmus and Pygocentrus: implications for the diversification of the Neotropical ichthyofauna, Molecular Ecology, vol.613, issue.10, pp.2115-2136, 2007.
DOI : 10.1007/BF00004815

N. Hubert, C. P. Meyer, H. J. Bruggemann, F. Guérin, R. J. Komeno et al., Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNAbarcoding provides new support to the Centre-of-Overlap hypothesis, PloS One, vol.7, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00722781

T. Huelsken, J. Keyse, L. Liggins, S. Penny, E. A. Treml et al., A Novel Widespread Cryptic Species and Phylogeographic Patterns within Several Giant Clam Species (Cardiidae: Tridacna) from the Indo-Pacific Ocean, PLoS ONE, vol.40, issue.11, p.80858, 2013.
DOI : 10.1371/journal.pone.0080858.s001

M. Hui, Connectivity and evolution of giant clams (Tridacnidae): a molecular genetic approach, 2012.

A. M. Jackson, K. Tenggardjaja, G. Perez, E. Azzurro, D. Golani et al., : a predictor of bioinvasion success?, Marine Ecology, vol.13, issue.4, 2015.
DOI : 10.1111/maec.12249

N. S. Jeena, Genetic divergence in lobsters (Crustacea: Palinuridae and Scyllaridae) from the Indian EEZ, 2013.

R. Kawahara, M. Miya, K. Mabuchi, S. Lavoue, J. G. Inoue et al., Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts, Molecular Phylogenetics and Evolution, vol.46, issue.1, pp.224-236, 2008.
DOI : 10.1016/j.ympev.2007.07.009

S. A. Mckenna and G. R. Allen, A Rapid Marine Biodiversity Assessment of Northwest Madagascar. Bulletin of the Rapid Assessment Program 31, Conservation International, 2003.

D. Obura, D. Carlo, G. Rabearisoa, A. Oliver, and T. , A rapid marine biodiversity assessment of the coral reefs of northeast Madagascar Conservation International, RAP Bulletin of Biological Assessment, vol.61, 2011.

R. Samoilys, . Reef, . Of, D. O. Madagascar-in-obura, T. Oliver et al., A Rapid Marine Biodiversity Assessment of the Coral Reefs of Northeast, 2011.

M. Anderson, R. C. Randall, J. E. Kuiter, and R. H. , Additions to the fish fauna of the Maldive Islands Part 2: New records of fishes from the Maldive Islands, with notes on other species, ? Ichthyological Bulletin of the J. L. B. Smith Institute of Ichthyology, vol.67, pp.20-32, 1998.

R. H. Kuiter, Photo Guide to Fishes of the Maldives, Atoll Editions, vol.257, 1998.

J. E. Randall and R. C. Anderson, Annotated checklist of the epipelagic and shorefishes of the Maldive Islands, Ichth. Bull., J.L.B. Smith Inst. Ichthyol, vol.59, pp.1-47, 1981.

J. E. Randall and R. C. Anderson, Annotated checklist of the epipelagic and shore fishes of the Maldive Islands, Ichthyol. Bull, vol.59, pp.1-47, 1993.

R. Mascarene-islands-fricke, Fishes of the Mascarene Islands (Réunion, Mauritius, and Rodrigues) An annotated checklist, with descriptions of new species, Koeltz Scientific Books, 1999.

Y. Letourneur, P. Chabanet, P. Durville, M. Taquet, E. Teissier et al., An updated checklist of the marine fish fauna of Reunion Island, South-Western Indian Ocean, Cybium, vol.28, pp.199-216, 2004.

R. C. Anderson, Developing Marine Reserves for Biodiversity Conservation and Sustainable Fisheries in Rodrigues, Impacts of Marine Reserves in Rodrigues: Report of a training visit to Shoals Rodrigues, p.pp, 2005.

E. Heemstra, P. C. Heemstra, M. J. Smale, T. Hooper, and D. Pelicier, Preliminary checklist of coastal fishes from the Mauritian island of Rodrigues, Journal of Natural History, vol.38, issue.23, pp.3315-3344, 2004.
DOI : 10.1080/00222930410001695088

M. Davidson, J. , N. Hill, L. Muaves, S. Mucaves et al., Vamizi Island Mozambique: Marine Ecological Assessment, 2006.

M. A. Pereira, Preliminary Checklist of Reef-associated Fishes of Mozambique, 2000.

M. A. Samoilys, I. Silva, J. Ndagala, S. Muciva, and D. Macharia, in press. A rapid assessment of coral reefs in Cabo Delgado, Mozambique. CORDIO Report

N. Rajaram, R. Nedumaran, and T. , Ichthyofaunal diversity in Great Nicobar Biosphere Reserve, Bay of Bengal, Journal of Threatened Taxa, vol.1, issue.3, pp.166-169, 2009.
DOI : 10.11609/JoTT.o1985.166-9

D. V. Rao, K. Devi, and P. T. Rajan, An account of ichthhyofauna of Niconar and Andaman islands, Bay of Bengal. Records of the Zoological Survey of India Occ, Paper, vol.178, pp.1-434, 2000.

S. J. Nw-australia-blaber, J. P. Salini, and D. T. Brewer, A checklist of fEshes from Albatross Bay and the Embley estuary, North-eastern Gulf of Carpentaria, Report, vol.210, p.22, 1990.

S. M. Oman-al-jufaili, G. Hermosa, S. S. Al-shuaily, A. Mujaini, and A. , ???????????? ???????????? ???????????? ?????????? ????????, Journal of King Abdulaziz University-Marine Sciences, vol.21, issue.1, pp.3-51, 2010.
DOI : 10.4197/Mar.21-1.1

J. E. Randall and D. Golani, Coastal fishes of Oman An annotated list of deep-sea fishes collected in the northern Red Sea, Gulf of Aqaba, Israel Journal of Zoology, vol.39, pp.299-336, 1993.

R. Bonfil and M. Abdallah, Field Identification Guide to the Sharks and Rays of the Red Sea and Gulf of Adan, FAO of the UN, 2004.

M. Dor, CLOFRES -Checklist of the Fishes of the Red Sea, Israel Academy of Sciences and Humanities, p.437, 1984.

D. Golani and S. V. Bogorodsky, The fishes of the Red Sea -Reappraisal and Updated Checklist Khalaf, pp.23-50, 2004.

J. E. Randall, Twenty two new records of fishes from the Red Sea. Fauna of Saudi Arabia, pp.259-275, 1994.

S. Smith, J. L. Smith, M. M. Smith, and M. M. , The Fishes of Seychelles. 215 p. Grahamstown: Rhodes Univ, The fishes of Seychelles, 1963.

S. Kemp and J. M. , Zoogeography of the coral reef fishes of the Socotra Archipelago, Journal of Biogeography, vol.63, issue.5, pp.919-933, 1998.
DOI : 10.1146/annurev.ecolsys.24.1.189

P. C. South-africa-heemstra and E. Heemstra, Coastal fishes of southern Africa, South African Institute for Aquatic Biodiversity (SAIAB) and National Inquiry Service Center (NISC), 2004.

M. M. Smith, P. C. Heemstra, and P. C. Heemstra, Smith's sea fishes Smith's sea fishes, 1986.

A. D. Wood, S. L. Brouwer, P. D. Cowley, and T. D. Harrison, An updated check list of the ichtyofaunal species assemblage of te Tsitsikamma national Park, Koedoe, vol.43, pp.88-95

M. M. Smith, Marine fishes of Maputaland In : Studies on the ecology of Maputaland, pp.164-187, 1980.

R. P. Van-des-elst, Shelf ichtyofauna of Natal In: Coastal ocean studies off Natal. South Africa, pp.209-225, 1988.

T. Lugendo, B. R. Nagelkerken, Y. Jiddawi, N. Mgaya, Y. N. Van-der-velde et al., Fish community composition of a tropical nonestuarine embayment in Zanzibar, Tanzania. Fisheries Sci, vol.73, pp.1213-1223, 2007.

T. Chavalit-vidthayanon, A. Siraprapha-premcharoen, and B. , The status of estuarine fish diversity in Thailand, Marine and Freshwater Research, vol.53, issue.2, pp.471-478, 2002.
DOI : 10.1071/MF01122

G. R. Allen and G. S. Stone, Rapid assessment survey of tsunami-affected reefs of Thailand, final technical report, 2005.

U. Satapoomin, A preliminary checklist of coral reef fishes of the Gulf of Thailand, South China Sea, The Raffles Bulletin of Zoology, vol.48, pp.31-53, 2000.

W. Australia-allen and G. R. , Fishes of the Montebello Islands Survey of the marine fauna and habitats of the Montebello Islands, Western Australia. Records of the Western Australian Museum Supplement No, J, vol.59, pp.47-57, 2000.

G. R. Allen, Fishes of Ashmore and Cartier Island Marine faunal survey of Ashmore Reef and Cartier Island, north-western Australia, pp.67-91, 1993.

G. R. Allen, New records of reef and shore fishes from north-western Australia. Records of the Western Australian Museum, pp.109-112, 1996.

G. R. Allen and B. C. Russell, Part VII. Fishes, Faunal Surveys of the Rowley Shoals, Scott Reef, and Seringapatam Reef, north-western Australia. Records of the Western Australian Museum, pp.79-103, 1986.

P. F. Berry, Historical background, description of the physical environments of Ashmore Reef and Cartier Island and notes on exploited species. Pp 1-11, Marine faunal survey of Ashmore Reef and Cartier Island, north-western Australia. Records of the Western Australian Museum, 1993.

J. B. Hutchins, Checklist of marine fishes of the Dampier Archipelago, Western Australia in, The Marine Flora and Fauna of Dampier, Western Australia. Western Australian Museum, pp.455-478, 2003.

J. B. Hutchins, Survey of the fishes of Ashmore Reef Report prepared for Parks Australia North, Western Australian Museum of Natural Science, 1998.

J. B. Hutchins, D. Williams, . Mcb, S. J. Newman, M. Cappo et al., New records of fishes for the Rowley Shoals and Scott/Seringapatam reefs, off north-western Australia, pp.119-123, 1995.

B. C. Russell and J. R. Hanley, The Biological Resources and Heritage Values of the Cartier and Hibernia Reef Systems, Timor Sea. Report of the Northern Territory Museum Cartier and Hibernia Reefs Expedition, Australian National Parks and Wildlife Service, 1992.

G. Al-absy and A. H. , Review of the goatfishes (Pisces: Perciformes: Mullidae) in the Gulf of Aqaba, Red Sea, Fauna of Saudi Arabia, pp.152-168, 1988.

G. R. Allen, Descriptions of two new species of damselfishes (Pomacentridae: Pomacentrus) from Madagascar, Journal of Ichthyology and Aquatic Biology, vol.6, pp.45-52, 2002.

G. R. Allen, N. Cross, C. Allen, and M. Gomon, Labridae: Wrasses. Zoological Catalogue of Australia, 2006.

G. R. Allen and J. E. Randall, A review of the damselfishes (Teleostei: Pomacentridae) of the Red Sea, Israel Journal of Zoology, vol.29, pp.1-98, 1980.

G. R. Allen and R. Steene, Reef Fishes of the Indian Ocean. A Pictorial Guide to the common reef fishes of the Indian Ocean, p.pp, 1988.

G. R. Allen, R. Steene, M. A. Allen, and D. Golani, Guide to Angelfishes and Butterflyfishes An annotated list on deep-sea fishes collected in the northern Red Sea, Gulf of Aqaba, Israel J. Zool, vol.39, pp.299-336, 1993.

M. E. Anderson and P. C. Heemstra, Review of the glassfishes (Perciformes: Ambassidae) of the western Indian Ocean, Cybium, vol.27, pp.199-209, 2003.

K. E. Carpenter, F. Krupp, D. A. Jones, U. K. Zajonz, and G. R. Allen, FAO species identification guide for fishery purposes. The living marine resources of Kuwait, Eastern Saudi Arabia, Bahrain, Qatar and the United Arab Emirates. FAO, Rome 293 pp. 17 colour plates Carpenter, FAO species catalogue. Emperor fishes and large-eye breams of the world (family Lethrinidae) An annotated and illustrated catalogue of Lethrinidae species known to date. FAO Fisheries Synopsis, 1989.

P. Chakrabarty and J. S. Sparks, Diagnoses for Leiognathus Lacep??de 1802, Equula Cuvier 1815, Equulites Fowler 1904, Eubleekeria Fowler 1904, and a New Ponyfish Genus (Teleostei: Leiognathidae), American Museum Novitates, vol.3623, issue.1, pp.1-11, 2008.
DOI : 10.1206/618.1

H. Debelius, Indian Ocean tropical fish guide, 321 pp. Aquaprint Verlags GmbH, 1993.

W. Fischer and G. Bianchi, FAO species identification sheets for fishery purposes. Western Indian Ocean (Fishing Area 51)

T. H. Fraser, Cardinalfishes of the genus Nectamia (Apogonidae, Perciformes) from the Indo-Pacific region with descriptions of four new species, Zootaxa, vol.1691, pp.1-52, 2008.

T. H. Fraser, J. E. Randall, and E. A. Lachner, A review of the Red Sea cardinalfishes of the Apogon bandanensis complex, with a description of a new species, Special Publication, J.L.B. Smith Institute of Ichthyology, vol.63, pp.1-13, 1999.

A. C. Gill, Revision of the Indo-Pacific dottyback fish subfamily Preudochromidae (Perciformes: Pseudochromidae) Smithiana Monograph, pp.1-213, 2004.

A. C. Gill and A. J. Edwards, Revision of the Indian Ocean Dottyback fish genera Chlidichthys and Pectinochromis (Perciformes: Pseudochromidae: Pseudoplesiopinae), Smithiana, Publication in Aquatic Biodiversity, vol.3, issue.46, p.pp, 2004.

A. C. Gill and R. Fricke, Revision of the western Indian Ocean fish subfamily Anisochrominae (Perciformes, Pseudochromidae), ? Bulletin of the Natural History Museum London (Zoology), vol.67, pp.191-207, 2001.

O. Gon and J. E. Randall, A review of the Cardinalfishes (Perciformes: Apogonidae) of the Red Sea, Smithiana Bulletin (The South African Institute for Aquatic Biodiversity. Grahamstown), vol.1, pp.1-46, 2003.

O. Gon and J. E. Randall, Revision of the Indo-Pacific Cardinalfishes genus Archamia (Perciformes: Apogonidae) with description of a new species. Indo-Pacific Fishes, pp.1-49, 2003.

P. C. Heemstra and J. E. Randall, Groupers of the World (Family Serranidae, Subfamily Epinephelinae) An annotated and illustrated catalogue of the grouper. FAO Fisheries Synopsis 125, 1993.

P. C. Heemstra and J. E. Randall, A review of the anthiine fish genus Plectranthias (Perciformes: Serranidae) of the western Indian Ocean, with description of a new species, and a key to the apecies, Smithiana Bulletin, vol.10, pp.3-17, 2009.

J. Herler and H. Hilgers, A synopsis of coral and coral-rock associated gobies (Pisces: Gobiidae) from Gulf of Aqaba, northern Red Sea, Aqua, vol.10, pp.103-132, 2005.

W. Holleman, A review of the triplefin fish genus Enneapterygius (Blennioidei: Tripterygiidae) in the western Indian Ocean, with descriptions of four new species, Smithiana, Publications in Aquatic Biodiversity, vol.5, pp.1-25, 2005.

W. Holleman, Fishes of the genus Helcogramma (Blennioidei: Tripterygiidae) in the western Indian Ocean, including Sri Lanka, with descriptions of four new species, ? Smithiana, Publications in Aquatic Biodiversity, Bulletin, vol.7, pp.51-81, 2007.

J. B. Hutchins, Review of the monacanthid fish genus Paramonacanthus, with descriptions of three new species. Records of the Western Australia Museum, pp.1-57, 1997.

T. Inoue and T. Nakabo, The Saurida undosquamis group (Aulopiformes: Synodontidae), with description of a new species from southern Japan, Ichthyological Research, vol.36, issue.340, pp.379-397, 2006.
DOI : 10.1007/s10228-006-0358-y

Z. Jaafar and J. E. Randall, A pictorial review and key to the shrimp gobies of the genus Amblyeleotris of the Red Sea, with description of a new species, Smithiana Bulletin, vol.10, pp.23-29, 2009.

L. W. Knapp, Review of the genus Coeciella Whitley (Teleostei: Platycephalidae) with the description of three new species, Proceedings of the Biological Society of Washington, pp.17-33, 1996.

R. H. Kuiter and T. Tonozuka, Pictorial guide to Indonesian reef fishes. Part 2. Fusiliers -Dragonets, Caesionidae -Callionymidae, pp.304-622, 2001.

R. H. Kuiter, Pipefishes of the syngnathid genus Dunckerocampus (Sygnathiformes: Syngnathidae), with a description of a new species from the Indian Ocean. ? Aqua, Journal of Ichthyology and Aquatic Biology, vol.3, pp.81-84, 1998.

R. H. Kuiter and J. E. Randall, Three look-alike Indo-Pacific labrid fishes, Halichoeres margaritaceus, H. nebulosus and H. miniatus, pp.13-18, 1981.

R. H. Kuiter, Fairy and rainbow wrasses and their relatives. A comprehensive guide to selected Labroids, 2002.

R. H. Kuiter, Seahorses, pipefishes and their relatives, 2000.

E. A. Lachner and S. J. Karnella, Fishes of the genus Eviota of the Red Sea with descriptions of three new species (Teleostei, Gobiidae), Smithsonian Contributions to Zoology, vol.286, issue.286, pp.1-23, 1978.
DOI : 10.5479/si.00810282.286

E. A. Lachner and S. J. Karnella, Fishes of the Indo-Pacific genus Eviota with descriptions of eight new species (Teleostei, Gobiidae), Smithsonian Contributions to Zoology, vol.315, issue.315, pp.1-127, 1980.
DOI : 10.5479/si.00810282.315

H. K. Larson, A revision of the commensal gobiid fish genera Pleurosicya and Luposicya (Gobiidae), with descriptions of eight new species of Pleurosicya and discussion of related genera, Beagle, Records of the Northern Territory Museum, vol.7, issue.1, pp.1-53, 1990.

S. A. Lourie, S. J. Foster, E. W. Cooper, and A. C. Vincent, A Guide to the Identification of Seahorses, 2004.

D. F. Markle and J. E. Olney, Systematics of the Pearlfishes (Pisces: Carapidae), Bulletin of Marine Science, vol.47, pp.269-410, 1990.

J. E. Mccosker, A revision of the snake-eel genus Callechelys (Anguilliformes: Ophichthidae) with the description of two new Indo- Pacific species and a new Callechelyin genus, Proceedings of the California Academy of Sciences, pp.50185-215, 1998.

A. G. Menon, A systematic monograph of the tongue soles of the genus Cynoglossus Hamilton-Buchanan (Pisces: Cynoglossidae) Smithsonian Contribution to Zoology, pp.1-129, 1977.

R. D. Mooi, Revision, phylogeny and discussion of biology and biogeography of the fish genus Plesiops (Perciformes: Plesiopidae), 1995.
DOI : 10.5962/bhl.title.53482

N. V. Parin, B. B. Collette, and Y. N. Shcherbachev, Beloniformes fishes of the world oceans, Trudy Okeanologii Instituta anUSSR, vol.97, pp.1-173, 1980.

J. E. Randall, A revision of the Indo-Pacific labrid genus Macropharyngodon, with descriptions of five new species, Pacific Science, vol.28, issue.4, pp.742-770, 1978.

J. E. Randall, A review of the labrid fish Genus Hologymnosus, pp.13-20, 1982.

J. E. Randall, Red Sea Fishes, IMMEL, vol.192, p.465, 1983.

J. E. Randall, Sharks of Arabia, IMMEL, vol.148, 1986.

J. E. Randall, Revision of the Indo-Pacific labrid fishes of the genus Coris, with description of five new species, Indo-Pacific Fishes, vol.29, pp.1-74, 1999.

J. E. Randall, Five new Indo-Pacific gobiid fishes of the genus Coryphopterus, Zoological Studies, vol.40, pp.206-225, 2001.

J. E. Randall, Surgeonfishes of Hawai'i and the World, 2001.

J. E. Randall, Revision of the goatfish genus Parupeneus (Perciformes: Mullidae), with descriptions of two new species, ? Indo-Pacific Fishes, vol.36, pp.1-64, 2004.

J. E. Randall and C. C. Baldwin, Revision of the serranid fishes of the subtribe Pseudogrammina, with descriptions of five new species. Indo-Pacific Fishes, pp.26-56, 1997.

J. E. Randall and R. W. Bruce, The parrotfishes of the subfamily Scarinae of the western Indian Ocean, with descriptions of three new species, Ichthyological Bulletin of the J.L.B. Smith Institute of Ichthyology, vol.47, pp.1-39, 1982.

J. E. Randall and K. D. Clements, Second revision of the surgeonfish genus Ctenochaetus (Perciformes: Acanthuridae), with descriptions of two new species, ? Indo-Pacific Fishes, vol.32, pp.1-33, 2001.

J. E. Randall and O. Gon, REVIEW OF THE SOLES OF THE GENUS ASERAGGODES OF THE WESTERN INDIAN OCEAN, WITH DESCRIPTIONS OF THREE NEW SPECIES, Israel Journal of Zoology, vol.51, issue.3, pp.165-190, 2006.
DOI : 10.1560/785N-CRCR-EXRG-MPAV

J. E. Randall and P. C. Heemstra, A review of the squirrelfishes of the subfamily Holocentrinae from the western Indian Ocean and Red Sea, ? Ichthyological Bulletin of the J. L. B. Smith Institute of Ichthyology, vol.49, issue.2, pp.1-27, 1985.

J. E. Randall and J. L. Earle, Review of Hawaiian Razorfishes of the Genus Iniistius (Perciformes: Labridae), Pacific Science, vol.56, issue.4, pp.389-402, 2002.
DOI : 10.1353/psc.2002.0038

J. E. Randall and W. N. Eschmeyer, Revision of the Indo-Pacific scorpionfish genus Scorpaenopsis, with descriptions of eight new species. Indo-Pacific Fishes, pp.1-79, 2001.

J. E. Randall and D. Golani, Review of the moray eels (Anguilliformes: Muraenidae) of the Red Sea, Bulletin of Marine Science, vol.56, pp.849-880, 1995.

J. E. Randall and M. Goren, A review of the gobioid fishes of the Maldive Islands, Ichthyological Bulletin, vol.58, pp.1-37, 1993.

J. E. Randall and P. C. Heemstra, Revision of Indo-Pacific groupers (Perciformes: Serranidae: Epinephelinae), with descriptions of five new species. Indo-Pacific Fishes, pp.1-332, 1991.

J. E. Randall, D. F. Hoese, J. E. Randall, and M. M. Smith, Revision of the Indo-Pacific genus Plectropomus (Percifermes: Serranidae) Indo-Pacific Fishes A review of the labrid fishes of the genus Halichoeres of the western Indian Ocean, with descriptions of six new species, Ichthyological Bulletin of the J.L.B. Smith Institute of Ichthyology, vol.45, pp.1-26, 1982.

J. E. Randall, K. Shao, and J. Chen, A review of the Indo-Pacific gobiid fish genus Ctenogobiops, with descriptions of two new species, Zoological Studies, vol.42, pp.506-515, 2003.

J. E. Randall, T. Shimizu, and T. Yamakawa, A revision of the holocentrid fish genus Ostichthys, with descriptions of four new species and a related new genus, Japanese Journal of Ichthyology, vol.29, pp.1-26, 1982.

J. E. Randall, J. T. Williams, and L. A. Rocha, The Indo-Pacific tetraodontid fish Canthigaster coronata, a complex of three species, Smithiana, Publications in Aquatic Biodiversity, vol.9, pp.3-13, 2008.

V. G. Ringer and J. T. Williams, The Indo-Pacific blenniid fish genus Istiblennius reappraised: a revision of Istiblennius, Blenniella, and Paralticus, new genus, ? Smithsonian Contributions to Zoology, vol.565, pp.1-193, 1994.

B. C. Russell and D. Golani, A review of the fish genus Parascolopsis (Nemipteridae) of the western Indian Ocean, with description of a new species from the northern Red Sea, Israel Journal of Zoology, vol.39, pp.337-347, 1993.

B. C. Russell, Revision of the Indo-Pacific labrid fish genus Suezichthys, with descriptions of four new species. Indo-Pacific Fishes, pp.1-21, 1985.

W. Schwarzhans and P. R. Møller, Teleostei: Bythitidae) of the Indo-west Pacific. Part III. Beaglichthys, Brosmolus, Monothrix and eight new genera with description of 20 new species, The Beagle, Records of the Museums and Art Galleries of the Northern Territory, pp.29-110, 2007.

W. Schwarzhans, P. R. Møller, and J. G. Nielsen, Review of the Dinematichthyini (Teleostei: Bythitidae) of the Indo-West Pacific. Part I. Diancistrus and two new genera with 26 new species, The Beagle, Records of the Museums and Art Galleries of the Northern Territory, pp.73-163, 2005.

W. F. Smith-vaniz, Revision of the jawfish genus Stalix (Pisces: Opistognathidae), with descriptions of four new species, Proceedings of the Academy of Natural Sciences Philadelphia, pp.375-407, 1989.

W. F. Smith-vaniz, New species of Indo-Pacific jawfishes (Opisthognathus: Opistognathidae) from the western Indian Ocean and Red Sea, ? Smithiana, Publications in Aquatic Biodiversity, Bulletin, vol.12, pp.39-54, 2010.

W. F. Smith-vaniz, The saber-toothed blennies, tribe Nemophini (Pisces: Blenniidae): an update, Proceedings of the Academy of Natural Sciences Philadelphia, pp.1-52, 1987.

V. G. Springer and J. T. Williams, The Indo-West Pacific blenniid fish genus Istiblenius reappraised: a revision of Istiblennius, Blenniella, and Paralticus, new genus, Smithsonian Contributions to Zoology, vol.565, pp.1-193, 1994.

F. Uiblein, Taxonomic review of western Indian Ocean goatfishes of the genus Mulloidichthys (Family Mullidae), with description of a new species and remarks on colour and body form variation in Indo-West Pacific species, ? Smithsiana, Publications in Aquatic Biodiversity Bulletin, vol.13, pp.51-73, 2011.

R. Winterbottom, Red Sea gobiid fishes of the genus Trimma, with the description of two new species, pp.93-98, 1995.

. Excoffier, Abbreviations for samples: as in Sample names arranged from West to East. WIO samples are EU, JN, MD and GL; the other Indian-Ocean sample is RS; Pacific-Ocean samples are PI, Table S3 Population-pairwise ? ST estimates, 1992.

L. Excoffier, Probability of ? ST value under null hypothesis of genetic homogeneity estimated from 1,000 random permutations under, 2010.

L. Tn, excluding 3 haplotypes of Za assigned to P. h. rubellus; NWIO included samples Om, Kollam included sample QLN of Jeena (2013); SriLanka included samples JSPHK and JSPHW of Senevirathna and Munasinghe (2014) (GENBANK nos. KC959890, KC959891 and KF548571) and sequences nos. KF715528-KF715550 and KF715552 from GENBANK; Chennai is sample CHE of Jeena (2013); Visakhapatnam included sample VSK of Jeena (2013) and sequence no. JN418937 from GENBANK; SChinaSea included samples Vn and Tw of Lavery et al. (2014) and sequences nos. JN542716 and JN591360 from GENBANK; Marquesas is sample M of Lavery Sample names arranged from West to East. Indian-Ocean samples other than WIO are: NWIO, Pacific-Ocean samples are SchinaSea and Marquesas. Table cells are toned grey, 2014.

. Excoffier, 1992) for Terapon jarbua, computed using ARLEQUIN 3.5 (Excoffier and Lischer, 2010) on the basis of partial CO1 gene sequences. Samples were constituted as following. Safrica included four individual sequences from Kwazulu-Natal (GENBANK nos. JF494663-JF494666); RedSea included two individual sequences from the Gulf of Eilat (GENBANK nos, Table S7 Population-pairwise ? ST estimates KJ466137, KJ466138); Eparses included seven new sequences from Juan de Nova; Yemen included all samples from Al-Mukalla and Socotra in Lavergne et al, 2014.

. Asgharian, 2011) (GENBANK nos HQ149959-HQ149961); Windia included a sequence published by Lakra, Gulf included three individual sequences from Bushehr, Persian Gulf FJ237549) and three individual sequences fom the western coast of the Indian peninsula (GENBANK nos. KC774674, KF268188 and KF268189); Eindia included four individual sequences from the eastern coast of the Indian peninsula (GENBANK nos. FJ265859, JX260979, KC241987 and KC417308); SchinaSea included two sequences from off southeastern China, 2011.

. Dist, Agrégation WA south of Shark Bay SW Australia -Aus-Mus

W. Scott and . Wa, Rowley shoals Northwest Transition Christmas & Cocos Maldives Chagos North Sumatra Rodrigues island Laccadives Andaman-Nicobar South Africa NE Mozambique Tanzania Kenya Mauritius La Reunion Madagascar all Comores-Mayotte and around Seychelles-Amirantes Aldabra-Carajos References

.. P. Borsa, I. S. Arlyza, W. Chen, J. Durand, M. G. Meekan et al., Resurrection of New Caledonian maskray Neotrygon trigonoides (Myliobatoidei: Dasyatidae) from synonymy with N.??kuhlii, based on cytochrome-oxidase I gene sequences and spotting patterns, Comptes Rendus Biologies, vol.336, issue.4, pp.221-232, 2013.
DOI : 10.1016/j.crvi.2013.05.005
URL : https://hal.archives-ouvertes.fr/ird-00847459

E. B. Brothers, D. Williams, . Mcb, and P. F. Sale, Length of larval life in twelve families of fishes at ?One Tree Lagoon?, Great Barrier Reef, Australia, Marine Biology, vol.65, issue.3, pp.319-324, 1983.
DOI : 10.1007/BF00393035

J. D. Dibattista, L. A. Rocha, M. T. Craig, K. A. Feldheim, and B. W. Bowen, Phylogeography of Two Closely Related Indo-Pacific Butterflyfishes Reveals Divergent Evolutionary Histories and Discordant Results from mtDNA and Microsatellites, Journal of Heredity, vol.103, issue.5, pp.617-629, 2012.
DOI : 10.1093/jhered/ess056

.. M. Gaither, B. Bowen, W. Bordenave, T. R. Rocha, L. A. 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, 2011.
DOI : 10.1186/1471-2148-11-189

M. R. Gaither, R. J. Toonen, D. R. Robertson, S. Planes, and B. W. 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, 2010.
DOI : 10.1111/j.1365-2699.2009.02188.x
URL : https://hal.archives-ouvertes.fr/hal-00609442

T. A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95, NT. Nucl. Acids Symp. Ser, vol.98, issue.41, pp.95-98, 1999.

M. Hui, Connectivity and evolution of giant clams (Tridacnidae): a molecular genetic approach, 2012.

S. C. Jameson, Early life-history of giant clams Tridacna crocea Lamarck, Tridacna maxima (Röding), and Hippopus hippopus (Linnaeus), Pac. Sci, vol.30, pp.219-232, 1976.

N. S. Jeena, Genetic divergence in lobsters (Crustacea: Palinuridae and Scyllaridae) from the Indian EEZ, 2013.

O. S. Klanten, J. H. Choat, and L. Van-herwerden, Extreme genetic diversity and temporal rather than spatial partitioning in a widely distributed coral reef fish, Marine Biology, vol.292, issue.Suppl., pp.659-670, 2007.
DOI : 10.1007/s00227-006-0372-7

M. Kulbicki, V. Parravicini, D. R. Bellwood, E. Arias-gonzàlez, P. Chabanet et al., Global Biogeography of Reef Fishes: A Hierarchical Quantitative Delineation of Regions, PLoS ONE, vol.5, issue.4, 2013.
DOI : 10.1371/journal.pone.0081847.s002

W. S. Lakra, M. S. Verma, M. Goswami, K. K. Lal, V. Mohindra et al., DNA barcoding Indian marine fishes, DNA barcoding Indian marine fishes, pp.60-71, 2011.
DOI : 10.1111/j.1755-0998.2010.02894.x

S. D. Lavery, A. Farhadi, H. Farahmand, T. Chan, A. Azhdehakoshpour et al., Evolutionary Divergence of Geographic Subspecies within the Scalloped Spiny Lobster Panulirus homarus (Linnaeus 1758), PLoS ONE, vol.6, issue.7, p.97247, 2014.
DOI : 10.1371/journal.pone.0097247.s001

P. Legendre and L. Legendre, Numerical ecology, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00530195

D. Muths, G. Gouws, M. Mwale, E. Tessier, and J. Bourjea, 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, G. Gouws, and J. Bourjea, Genetic structure of the reef grouper Epinephelus merra in the West Indian Ocean appears congruent with biogeographic and oceanographic boundaries, Mar. Ecol, 2014.

B. F. Phillips and H. Matsuda, A Global Review of Spiny Lobster Aquaculture, Recent advances and new species in aquaculture, pp.22-84, 2011.
DOI : 10.1002/9781444341775.ch2

J. Senevirathna and D. Munasinghe, Genetic diversity and population structure of Panulirus homarus populations of Southern Sri Lanka and South India revealed by the mitochondrial COI gene region, Proc. Int. Conf. Food, 2014.

C. A. Sims, C. Riginos, S. P. Blomberg, T. Huelsken, J. Drew et al., Cleaning up the biogeography of Labroides dimidiatus using phylogenetics and morphometrics, Coral Reefs, vol.28, issue.1, pp.223-233, 2014.
DOI : 10.1007/s00338-013-1093-2

A. C. Stier, A. W. Hein, V. Parravicini, and M. Kulbicki, Larval dispersal drives trophic structure across Pacific coral reefs, Nature Communications, vol.216, p.5575, 2014.
DOI : 10.1111/j.1095-8649.2003.00214.x

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-2729, 2013.
DOI : 10.1093/molbev/mst197

N. M. Whitney, W. D. Robbins, J. K. Schultz, B. W. Bowen, and K. N. Holland, Oceanic dispersal in a sedentary reef shark (Triaenodon obesus): genetic evidence for extensive connectivity without a pelagic larval stage, Journal of Biogeography, vol.93, issue.45, pp.1144-1156, 2012.
DOI : 10.1111/j.1365-2699.2011.02660.x

K. L. Winters, L. Van-herwerden, J. H. Choat, and D. R. 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

S. Wright, Isolation by distance, Genetics, vol.28, pp.114-138, 1942.

M. Yamaguchi, Early life history of coral reef asteroids, with special reference to Acanthaster planci (L.) Biology and geology of coral reefs, pp.369-389, 1973.