S. Akimoto, S. Itoi, S. Sezaki, P. Borsa, and S. Watabe, Identification of alfonsino, Beryx mollis and B. splendens collected in Japan, based on the mitochondrial cytochrome b gene, and their comparison with those collected in New Caledonia, Fisheries Science, vol.5, issue.1, pp.202-207, 2006.
DOI : 10.1007/BF00346305

A. Bremer, J. Stequert, B. Robertson, N. , and E. B. , Genetic evidence for inter-oceanic subdivision of bigeye tuna ( Thunnus obesus ) populations, Marine Biology, vol.132, issue.4, pp.547-557, 1998.
DOI : 10.1007/s002270050420

S. Arnaud, F. Bonhomme, and P. Borsa, Mitochondrial DNA analysis of the genetic relationships among populations of scad mackerel ( Decapterus macarellus , D. macrosoma , and D. russelli ) in South-East Asia, Marine Biology, vol.135, issue.4, pp.699-707, 1999.
DOI : 10.1007/s002270050671

J. Avise, J. Arnold, R. Ball, E. Bermingham, T. Lamb et al., Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics, Annual Review of Ecology and Systematics, vol.18, issue.1, pp.489-522, 1987.
DOI : 10.1146/annurev.es.18.110187.002421

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

URL : https://academic.oup.com/mbe/article-pdf/16/1/37/11164892/mbev_16_01_0037.pdf

P. Barber, M. Erdmann, and S. Palumbi, COMPARATIVE PHYLOGEOGRAPHY OF THREE CODISTRIBUTED STOMATOPODS: ORIGINS AND TIMING OF REGIONAL LINEAGE DIVERSIFICATION IN THE CORAL TRIANGLE, Evolution, vol.92, issue.2, pp.1825-1839, 2006.
DOI : 10.1007/s002270050468

L. Bay, J. Choat, L. Van-herwerden, and D. Robertson, High genetic diversities and complex genetic structure in an Indo-Pacific tropical reef fish (Chlorurus sordidus): evidence of an unstable evolutionary past?, Marine Biology, vol.144, issue.4, pp.757-767, 2003.
DOI : 10.1007/s00227-003-1224-3

G. Begg, C. Keenan, and M. Sellin, Genetic variation and stock structure of school mackerel and spotted mackerel in northern Australian waters, Journal of Fish Biology, vol.4, issue.3, pp.543-559, 1998.
DOI : 10.1577/1548-8659(1997)126<0369:AECOSI>2.3.CO;2

K. Belkhir, P. Borsa, L. Chikhi, N. Raufaste, and F. Bonhomme, GENETIX 4.05, Logiciel sous WINDOWS TM pour la Génétique des Populations, Laboratoire Génome, issue.2, 2004.

J. Benzie, Major genetic differences between crown-of-thorns starfish (Acanthaster planci) populations in the Indian and Pacific Oceans, Evolution, vol.53, pp.1782-1795, 1999.

G. Bernardi, S. Holbrook, R. Schmitt, N. Crane, and E. Demartini, Species boundaries, populations and colour morphs in the coral reef three-spot damselfish (Dascyllus trimaculatus) species complex, Proceedings of the Royal Society B: Biological Sciences, vol.269, issue.1491, pp.599-605, 2002.
DOI : 10.1098/rspb.2001.1922

P. Borsa, Genetic structure of round scad mackerel Decapterus macrosoma (Carangidae) in the Indo-Malay archipelago, Marine Biology, vol.142, issue.3, pp.575-581, 2003.
DOI : 10.1007/s00227-002-0974-7

URL : https://hal.archives-ouvertes.fr/hal-00554436

B. Bowen, A. Muss, L. Rocha, and W. Grant, Shallow mtDNA Coalescence in Atlantic Pygmy Angelfishes (Genus Centropyge) Indicates a Recent Invasion from the Indian Ocean, Journal of Heredity, vol.97, issue.1, pp.1-12, 2006.
DOI : 10.1093/jhered/esj006

J. Briggs, Fishes of Worldwide (Circumtropical) Distribution, Copeia, vol.1960, issue.3, pp.171-180, 1960.
DOI : 10.2307/1439652

J. Briggs, Marine Zoogeography, 1974.

R. Broughton, L. Stewart, and J. Gold, Microsatellite variation suggests substantial gene flow between king mackerel (Scomberomorus cavalla) in the western Atlantic Ocean and Gulf of Mexico, Fisheries Research, vol.54, issue.3, pp.305-316, 2002.
DOI : 10.1016/S0165-7836(01)00275-2

R. Buckworth, S. Newman, J. Ovenden, R. Lester, and G. Mcpherson, The stock structure of northern and western Australian Spanish mackerel. Final report, Fisheries Research & Development Corporation Project Department of Primary Industry, Fisheries and Mines, Northern Territory Government, Australia. Fishery Report, vol.159, issue.225, pp.i-vi, 1998.

V. Buonaccorsi, E. Starkey, and J. Graves, Mitochondrial and nuclear DNA analysis of population subdivision among young-of-the-year Spanish mackerel ( Scomberomorus maculatus ) from the western Atlantic and Gulf of Mexico, Marine Biology, vol.138, issue.1, pp.37-45, 2001.
DOI : 10.1007/s002270000439

L. Cárdenas, C. Hernández, E. Poulin, A. Magoulas, I. Kornfield et al., Origin, diversification, and historical biogeography of the genus Trachurus (Perciformes: Carangidae), Molecular Phylogenetics and Evolution, vol.35, issue.2, pp.496-507, 2005.
DOI : 10.1016/j.ympev.2005.01.011

K. Carpenter and V. Niem, FAO species identification guide for fishery purposes. The living marine resources of the Western Central Pacific Bony fishes part 4 (Labridae to Latimeriidae), estuarine crocodiles, sea turtles, sea snakes and marine mammals, pp.3381-4218, 2001.

J. Gold, A. Jobity, E. Saillant, and M. Renshaw, Population structure of carite (Scomberomorus brasiliensis) in waters offshore of Trinidad and northern Venezuela, Fisheries Research, vol.103, issue.1-3, pp.30-39, 2010.
DOI : 10.1016/j.fishres.2010.01.009

J. Gold, Á. Kristmundsdóttir, and L. Richardson, Mitochondrial DNA variation in king mackerel ( Scomberomorus cavalla ) from the western Atlantic Ocean and Gulf of Mexico, Marine Biology, vol.129, issue.2, pp.221-223, 1997.
DOI : 10.1007/s002270050163

J. Gold, E. Pak, and D. Devries, Population structure of king mackerel (Scomberomorus cavalla) around peninsular Florida, as revealed by microsatellite DNA, Fishery Bulletin, vol.100, pp.491-509, 2002.

E. Gonzalez, P. Beerli, and R. Zardoya, Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839), BMC Evolutionary Biology, vol.8, issue.1, p.252, 2008.
DOI : 10.1186/1471-2148-8-252

URL : https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/1471-2148-8-252?site=bmcevolbiol.biomedcentral.com

J. Graves, Molecular insights into the population structures of cosmopolitan marine fishes, Journal of Heredity, vol.89, issue.5, pp.427-437, 1998.
DOI : 10.1093/jhered/89.5.427

T. Hall, BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95, NT. Nucleic Acids Symposium Series, vol.98, issue.41, pp.95-98, 1999.

M. Hasegawa, K. 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.160-174, 1985.
DOI : 10.1016/B978-1-4832-2734-4.50017-6

J. Hoolihan, P. Anandh, and L. Van-herwerden, Mitochondrial DNA analyses of narrow-barred Spanish mackerel (Scomberomorus commerson) suggest a single genetic stock in the ROPME sea area (Arabian Gulf, Gulf of Oman, and Arabian Sea), ICES Journal of Marine Science, vol.63, pp.1066-1074, 2006.
DOI : 10.1016/j.icesjms.2006.03.012

J. Horne, L. Van-herwerden, H. 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

R. Hudson, Gene genealogies and the coalescent process. Pp. 1-44 in D Futuyma and J Antonovics. Oxford surveys in evolutionary biology, 1990.

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980.
DOI : 10.1038/scientificamerican1179-98

S. Klanten, L. Van-herwerden, and J. Choat, 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 : 10.1093/oxfordjournals.molbev.a025731

N. Knowlton, Sibling Species in the Sea, Annual Review of Ecology and Systematics, vol.24, issue.1, pp.189-216, 1993.
DOI : 10.1146/annurev.es.24.110193.001201

N. Knowlton, Molecular genetic analyses of species boundaries in the sea, Hydrobiologia, vol.420, pp.73-90, 2000.
DOI : 10.1007/978-94-017-2184-4_8

M. Kochzius and A. Nuryanto, across the Indo-Malay Archipelago: implications related to evolutionary processes and connectivity, Molecular Ecology, vol.2, issue.4), pp.3775-3787, 2008.
DOI : 10.5670/oceanog.2005.01

W. Lee, J. Conroy, W. Howell, and T. Kocher, Structure and evolution of teleost mitochondrial control regions, Journal of Molecular Evolution, vol.41, issue.1, pp.54-66, 1995.
DOI : 10.1007/BF00174041

H. Lessios, The Great American Schism: Divergence of Marine Organisms After the Rise of the Central American Isthmus, Annual Review of Ecology, Evolution, and Systematics, vol.39, issue.1, pp.63-91, 2008.
DOI : 10.1146/annurev.ecolsys.38.091206.095815

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1452, 2009.
DOI : 10.1093/bioinformatics/btp187

S. Lourie, D. Green, and A. Vincent, Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus), Molecular Ecology, vol.103, issue.eds Lessios HA, pp.1073-1094, 2005.
DOI : 10.1111/j.0014-3820.2001.tb00760.x

C. Lu, C. Chen, C. Hui, T. Tzeng, and S. Yeh, Population genetic structure of the swordfish, Xiphias gladius, in the Indian Ocean and West Pacific inferred from the complete DNA sequence of the mitochondrial control region, Zoological Studies, vol.45, pp.269-279, 2006.

A. Magoulas, N. Tsimenides, and E. Zouros, Mitochondrial DNA phylogeny and the reconstruction of the population history of a species: the case of the European anchovy (Engraulis encrasicolus), Molecular Biology and Evolution, vol.13, issue.1, pp.178-190, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025554

A. Mccune and N. Lovejoy, The relative rate of sympatric and allopatric speciation in fishes: tests using DNA sequence divergence between sister species and among clades, 1998.

M. M. Nei and W. Li, Molecular evolutionary genetics Mathematical model for studying genetic variation in terms of restriction endonucleases, Proceedings of the National Academy of Sciences of the, pp.5269-5273, 1979.

C. Nesbø, E. Rueness, S. Iversen, D. Skagen, and K. Jakobsen, Phylogeography and population history of Atlantic mackerel (Scomber scombrus L.): a genealogical approach reveals genetic structuring among the eastern Atlantic stocks, Proceedings of the Royal Society B: Biological Sciences, vol.267, issue.1440, pp.281-292, 2000.
DOI : 10.1098/rspb.2000.0998

J. Ovenden, J. Salini, O. Connor, S. Street, and R. , Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle, Molecular Ecology, vol.11, issue.7, pp.1991-1999, 2004.
DOI : 10.1111/j.0014-3820.2002.tb01348.x

S. Palumbi, Genetic Divergence, Reproductive Isolation, and Marine Speciation, Annual Review of Ecology and Systematics, vol.25, issue.1, pp.547-572, 1994.
DOI : 10.1146/annurev.es.25.110194.002555

S. Palumbi, A. Martin, S. Romano, W. Mcmillan, L. Stice et al., The simple fool " s guide to PCR, version 2.0, 1991.

C. Perrin and P. Borsa, Mitochondrial DNA analysis of the geographic structure of Indian scad mackerel in the Indo-Malay archipelago, Journal of Fish Biology, vol.2, issue.5, pp.1421-1426, 2001.
DOI : 10.1007/s002270000379

URL : https://hal.archives-ouvertes.fr/ird-00288428

M. Raymond and F. Rousset, GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism, Journal of Heredity, vol.86, issue.3, pp.248-249, 1995.
DOI : 10.1093/oxfordjournals.jhered.a111573

URL : https://hal.archives-ouvertes.fr/halsde-00186383

W. Rice, ANALYZING TABLES OF STATISTICAL TESTS, Evolution, vol.6, issue.1, pp.223-225, 1989.
DOI : 10.1007/978-1-4613-8122-8

A. Rohfritsch and P. Borsa, Genetic structure of Indian scad mackerel Decapterus russelli: Pleistocene vicariance and secondary contact in the Central Indo-West Pacific Seas, Heredity, vol.118, issue.4, pp.315-326, 2005.
DOI : 10.1016/0003-2697(81)90179-2

URL : https://hal.archives-ouvertes.fr/hal-00554479

P. Rosel and B. Block, Mitochondrial control region variability and global population structure in the swordfish, Xiphias gladius, Marine Biology, vol.52, issue.1, pp.11-22, 1996.
DOI : 10.1146/annurev.es.18.110187.002421

J. Shaklee, S. Phelps, and J. Salini, Analysis of fish stock structure and mixed-stock fisheries by the electrophoretic characterization of allelic isozymesApplication of electrophoretic and isoelectric focusing techniques in fisheries management, pp.173-196, 1990.

B. Shui, Z. Han, T. Gao, Z. Miao, and T. Yanagimoto, Mitochondrial DNA variation in the East China Sea and Yellow Sea populations of Japanese Spanish mackerel Scomberomorus niphonius, Fisheries Science, vol.409, issue.3, pp.593-600, 2009.
DOI : 10.1007/s12562-009-0083-3

C. Stepien, J. Randall, and R. Rosenblatt, Genetic and morphological divergence of a circumtropical complex of goatfishes: Mulloidichthys vanicolensis, M. dentatus, and M. martinicus, Pacific Science, vol.48, pp.44-56, 1994.

Z. Sulaiman and J. Ovenden, Population genetic evidence for the east???west division of the narrow-barred Spanish mackerel (Scomberomorus commerson, Perciformes: Teleostei) along Wallace???s Line, Biodiversity and Conservation, vol.27, issue.Supplement B, pp.563-574, 2009.
DOI : 10.1007/s10531-009-9699-y

F. Tajima, Evolutionary relationship of DNA sequences in finite populations, Genetics, vol.105, pp.437-460, 1983.

F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.

K. Tamura, Estimation of the number of nucleotide substitutions when there are strong transitiontransversion and G+C-content biases, Molecular Biology and Evolution, vol.9, pp.678-687, 1992.

K. Tamura and M. Nei, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Molecular Biology and Evolution, vol.10, pp.512-526, 1993.

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA 5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Molecular Biology and Evolution, 2011.
DOI : 10.1093/molbev/msr121

URL : https://academic.oup.com/mbe/article-pdf/28/10/2731/2954190/msr121.pdf

M. Taylor and M. Hellberg, Genetic Evidence for Local Retention of Pelagic Larvae in a Caribbean Reef Fish, Science, vol.299, issue.5603, pp.107-109, 2003.
DOI : 10.1126/science.1079365

T. Theisen, B. Bowen, W. Lanier, and J. Baldwin, (tuna family Scombridae), Molecular Ecology, vol.4, issue.12, pp.4233-4247, 2008.
DOI : 10.18785/gcr.1501.06

J. Timm, M. Figiel, and M. Kochzius, Contrasting patterns in species boundaries and evolution of anemonefishes (Amphiprioninae, Pomacentridae) in the centre of marine biodiversity, Molecular Phylogenetics and Evolution, vol.49, issue.1, pp.268-276, 2008.
DOI : 10.1016/j.ympev.2008.04.024

L. Van-herwerden, J. Mcilwain, H. Oufi, W. Al-amry, and A. Reyes, Development and application of microsatellite markers for Scomberomorus commerson (Perciformes; Teleostei) to a population genetic study of Arabian Peninsula stocks, Fisheries Research, vol.79, issue.3, pp.258-266, 2006.
DOI : 10.1016/j.fishres.2006.04.004

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 : 10.1038/35022565

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

J. Viñas, A. Bremer, J. Pla, and C. , Inter-oceanic genetic differentiation among albacore (Thunnus alalunga) populations, Marine Biology, vol.145, pp.225-232, 2004.

B. Weir and C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, vol.38, pp.822-831, 1984.

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 : 10.1098/2004.3005

. Gold, &. Kristmundsdóttir, and . Richardson, S. commerson Persian Gulf ? Oman Sea CR, 1997.
URL : https://hal.archives-ouvertes.fr/in2p3-00128976

A. &. Hoolihan and . Van-herwerden, S. commerson Tropical SW Pacific CR, sequence 0.306-0.586 present study S. maculatus W Atlantic and Gulf of Mexico ND4, 2006.

. Buonaccorsi, &. Starkey, and . Graves, S. niphonius East China Sea ? Yellow Sea CR, 2001.

. Shui, S. sierra Pacific coast of Tropical America CR, 2009.

D. López, U. Alcocer, and &. Jaimes, Nuclear S. brasiliensis Southern Caribbean Sea 8 microsatellite loci* 0.002 Gold et al. (2010) S. cavalla W Atlantic and Gulf of Mexico 5 microsatellite, 2010.

. Broughton, &. Stewart, and . Gold, S. cavalla Around peninsular Florida 5 microsatellite loci, 2002.

. Gold, &. Pak, and . Devries, S. commerson Persian Gulf ? Oman Sea 5 microsatellite loci* 0.029 van Herwerden et al. (2006) S. commerson Tropical Australia ? Papua New Guinea 9 allozyme loci* 0, J.B. Shaklee in Buckworth et al, p.0, 2002.
URL : https://hal.archives-ouvertes.fr/in2p3-00128976

. Buonaccorsi, &. Starkey, and . Graves, S. munroi Northern and Eastern Australia 7 allozyme loci* 0, p.38, 2001.

. Begg, &. Keenan, and . Sellin, S. queenslandicus Northern and Eastern Australia 7 allozyme loci, 1998.

*. Only and . Loci, where estimated allele frequencies <0.95 in at least one population) were considered in this count Figure 1. Narrow-barred Spanish mackerel, Scomberomorus commerson. Sampling locations across the Indo-West pacific. Pie diagrams represent control-region haplotype frequencies (hatchured Clade I; black: Haplogroup ii; dark grey: Subclade IIa

S. Iib, J. , J. Sea, . Bali, . Bali et al., Subclade IIc; pale grey: Subclade IId; see Fig. 2) Abbreviations for samples, Anandh & van Herwerden, vol.white, 1984.

. Tamura, Median-joining parsimony network (Bandelt, Forster & Röhl, 1999) of control region haplotypes. Groups of haplotypes delineated according to genetic proximity, with indication of area of occurrence; two main clades numbered I and II, the latter with sub-clades IIa, IIb, IIc and IId radiating from a central haplogroup II. Branch length proportional to number of mutational steps; closed circles represent individual haplotypes, their area being proportional to their frequency in the total sample; arrow indicates root Bootstrap support (Neighbour-Joining algorithm; Kimura- 2 parameter distances; 1000 resampling runs) was: 100% for clade I; 98% for sub-clade IIa; 32% for sub-clade IIb, Figure 2. Narrow-barred Spanish mackerel, Scomberomorus commerson for sub-clade IIc; 98% for Sub-clade IId. Scale bar: 5 mutational steps, 2007.