R. Abbott, D. Albach, S. Ansell, J. W. Arntzen, S. J. Baird et al., Hybridization and speciation, Journal of Evolutionary Biology, vol.9, issue.2, pp.229-275, 2013.
DOI : 10.1186/1471-2148-9-83
URL : https://hal.archives-ouvertes.fr/hal-01945468

D. C. Adams, E. Et, and . Otarola-castillo, package for the collection and analysis of geometric morphometric shape data, Methods in Ecology and Evolution, vol.60, issue.4, pp.393-399, 2013.
DOI : 10.1111/j.0014-3820.2006.tb01160.x

R. C. Albertson, T. D. Et, and . Kocher, GENETIC ARCHITECTURE SETS LIMITS ON TRANSGRESSIVE SEGREGATION IN HYBRID CICHLID FISHES, Evolution, vol.18, issue.3, pp.686-90, 2005.
DOI : 10.1146/annurev.es.12.110181.000323

G. H. Albrecht, Multivariate Analysis and the Study of Form, with Special Reference to Canonical Variate Analysis, American Zoologist, vol.20, issue.4, pp.679-693, 1980.
DOI : 10.1093/icb/20.4.679

T. D. Als, M. M. Hansen, G. E. Maes, M. Castonguay, L. Riemann et al., All roads lead to home: panmixia of European eel in the Sargasso Sea, «All roads lead to home: panmixia of European eel in the Sargasso Sea, pp.1333-1346, 2011.
DOI : 10.1038/35059079

M. L. Arnold, S. A. Et, and . Hodges, Are natural hybrids fit or unfit relative to their parents?, Trends in Ecology & Evolution, vol.10, issue.2, pp.67-71, 1995.
DOI : 10.1016/S0169-5347(00)88979-X

N. Backstrom, G. P. Saetre, and E. H. Ellegren, Inferring the demographic history of European Ficedula flycatcher populations, BMC Evolutionary Biology, vol.13, issue.1, 2013.
DOI : 10.1038/nature04226

N. A. Baird, P. D. Etter, T. S. Atwood, M. C. Currey, A. L. Shiver et al., Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers, «Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers, p.3376, 2008.
DOI : 10.1371/journal.pone.0003376.g003
URL : https://doi.org/10.1371/journal.pone.0003376

N. H. Barton, The dynamics of hybrid zones, Heredity, vol.43, issue.3, pp.341-359, 1979.
DOI : 10.1038/hdy.1979.87

N. H. Barton, The hybrid sink effect, «The Hybrid Sink Effect, pp.277-278, 1980.
DOI : 10.1038/hdy.1980.23

N. H. Barton, G. M. Et, and . Hewitt, Analysis of Hybrid Zones, Annual Review of Ecology and Systematics, vol.16, issue.1, pp.113-148, 1985.
DOI : 10.1146/annurev.es.16.110185.000553

N. H. Barton, K. S. Et, and . Gale, «Genetic Analysis of Hybrid Zones.» Dans Hybrid Zones and the Evolutionary Process, pp.14-45, 1993.

N. Barton, B. O. Et, and . Bengtsson, The barrier to genetic exchange between hybridising populations, «The Barrier to Genetic Exchange between Hybridizing Populations, pp.357-376, 1986.
DOI : 10.1038/hdy.1986.135

M. A. Beaumont, W. Zhang, and D. J. Balding, «Approximate Bayesian computation in population genetics, Genetics, vol.162, pp.2025-2060, 2002.

R. Bedoui, «Elevage de Solea senegalensis (Kaup, 1958) en Tunisie.» Marine aquaculture finfish species diversification, Proceedings of the seminar of the CIHEAM Network on Technology of Aquaculture in the Mediterranean (TECAM), pp.14-17, 1995.

K. Belkhir, P. Borsa, L. Chikhi, N. Raufaste, and E. F. Bonhomme, «GENETIX 4.05, Logiciel Sous Windows TM Pour Al Genetique De Populations, 1996.

M. A. Bell, M. P. Et, and . Travis, Hybridization, transgressive segregation, genetic covariation, and adaptive radiation, Trends in Ecology & Evolution, vol.20, issue.7, pp.358-61, 2005.
DOI : 10.1016/j.tree.2005.04.021

N. Bierne, J. Welch, E. Loire, F. Bonhomme, and E. P. David, The coupling hypothesis: why genome scans may fail to map local adaptation genes, Molecular Ecology, vol.17, issue.Suppl 1, pp.2044-72, 2011.
DOI : 10.1111/j.1365-294X.2008.03755.x

N. Bierne, P. A. Gagnaire, and E. P. David, The geography of introgression in a patchy environment and the thorn in the side of ecological speciation, Current Zoology, vol.59, issue.1, pp.72-86, 2013.
DOI : 10.1093/czoolo/59.1.72

N. Bierne, P. Borsa, C. Daguin, D. Jollivet, F. Viard et al., Introgression patterns in the mosaic hybrid zone between Mytilus edulis and M. galloprovincialis, Molecular Ecology, vol.112, issue.2, pp.447-461, 2003.
DOI : 10.1007/BF00356285

N. Bierne, T. Lenormand, F. Bonhomme, and P. David, Deleterious mutations in a hybrid zone: can mutational load decrease the barrier to gene flow?, Genetical Research, vol.80, issue.3, pp.197-204, 2002.
DOI : 10.1017/S001667230200592X

P. Borsa, J. P. Et, and . Quignard, «Systematics of the Atlantic-Mediterranean soles Pegusa impar, Plascaris , Solea aegyptiaca, S-senegalensis, and S-solea (Pleuronectiformes : Soleidae), » Canadian Journal of Zoology-Revue Canadienne De Zoologie, vol.79, pp.2297-2302, 2001.

B. Boutier, J. F. Chiffoleau, J. L. Gonzalez, P. Lazure, D. Auger et al., «Influence of the Gironde estuary outputs on cadmium concentrations in the coastal waters: consequences on the Marennes-Oleron bay (France).» Oceanologica Acta, pp.745-757, 2000.

J. Casellas, R. J. Gularte, C. R. Farber, L. Varona, M. Mehrabian et al., Genome Scans for Transmission Ratio Distortion Regions in Mice, Genetics, vol.191, issue.1, pp.247-59, 2012.
DOI : 10.1534/genetics.111.135988

J. M. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. H. Postlethwait, From Short-Read Sequences, G3: Genes|Genomes|Genetics, vol.1, issue.3, pp.171-82, 2011.
DOI : 10.1534/g3.111.000240

B. Charlesworth, M. T. Morgan, and E. D. Charlesworth, «The effect of deleterious mutations on neutral molecular variation, Genetics, vol.134, pp.1289-303, 1993.

C. Christe, K. N. Stolting, L. Bresadola, B. Fussi, B. Heinze et al., fertility and recurrent gene flow, Molecular Ecology, vol.14, issue.11, pp.2482-98
DOI : 10.1046/j.1420-9101.2001.00335.x

J. A. Coyne and H. A. Orr, Speciation, vol.37, 2004.

T. E. Cruickshank and M. W. Hahn, Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow, Molecular Ecology, vol.110, issue.13, pp.3133-3157, 2014.
DOI : 10.1073/pnas.1219381110

P. Danecek, A. Auton, G. Abecasis, C. A. Albers, E. Banks et al., The variant call format and VCFtools, Bioinformatics, vol.11, issue.9, pp.2156-2164, 2011.
DOI : 10.1101/gr.107524.110

P. V. Debes, F. E. Zachos, and E. R. Hanel, L., Clupeidae) reveals isolated climatically vulnerable populations in the Mediterranean Sea and range expansion in the northeast Atlantic, Molecular Ecology, vol.28, issue.17, pp.3873-88, 2008.
DOI : 10.1093/icesjms/45.2.165

E. P. Derryberry, G. E. Derryberry, J. M. Maley, and R. T. Brumfield, : hybrid zone analysis using an R software package, Molecular Ecology Resources, vol.45, issue.3, pp.652-663, 2014.
DOI : 10.2307/2409660

D. Meniger and M. , «Révision systématique des genres de la famille des Soleidae presents sur les côtes de l'Est-Atlantique et de la Méditerranée, 1997.

P. G. Digby and . Et-rodney-alistair-kempton, Multivariate analysis of ecological communities, 1987.

T. Dobzhansky, «Genetic nature of species differences, Am. Nat, vol.71, pp.404-420, 1937.

S. Dray, D. Chessel, and E. J. Thioulouse, Procrustean co-inertia analysis for the linking of multivariate datasets, ??coscience, vol.10, issue.1, pp.110-119, 2003.
DOI : 10.1007/BF02289009

S. Dray, A. B. Et, and . Dufour, «The ade4 package: Implementing the duality diagram for ecologists, Journal of Statistical Software, vol.22, pp.1-20, 2007.

S. Edmands, HETEROSIS AND OUTBREEDING DEPRESSION IN INTERPOPULATION CROSSES SPANNING A WIDE RANGE OF DIVERGENCE, Evolution, vol.10, issue.168, pp.1757-1768, 1999.
DOI : 10.1111/j.1558-5646.1955.tb01539.x

H. Ellegren, L. Smeds, R. Burri, P. I. Olason, N. Backstrom et al., The genomic landscape of species divergence in Ficedula flycatchers, Nature, vol.117, issue.7426, pp.756-60, 2012.
DOI : 10.1159/000103165

G. Ewing and J. Hermisson, MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus, Bioinformatics, vol.175, issue.16, pp.2064-2065, 2010.
DOI : 10.1534/genetics.106.064642

J. L. Feder, P. Et, and . Nosil, THE EFFICACY OF DIVERGENCE HITCHHIKING IN GENERATING GENOMIC ISLANDS DURING ECOLOGICAL SPECIATION, Evolution, vol.175, issue.6, pp.1729-1776, 2010.
DOI : 10.1111/j.0014-3820.2004.tb00490.x

J. L. Feder, S. P. Egan, and E. P. Nosil, «The genomics of speciation-with-gene-flow.» Trends Genet, pp.342-50, 2012.

P. A. Gagnaire, E. Normandeau, S. A. Pavey, and E. L. Bernatchez, Molecular Ecology, vol.169, issue.11, pp.3036-3048, 2013.
DOI : 10.1534/genetics.104.032573

P. A. Gagnaire, S. A. Pavey, E. Normandeau, and E. L. Bernatchez, THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING, Evolution, vol.17, issue.9, pp.2483-97, 2013.
DOI : 10.1111/j.1365-294X.2008.03755.x

L. Gay, P. A. Crochet, D. A. Bell, and T. Lenormand, COMPARING CLINES ON MOLECULAR AND PHENOTYPIC TRAITS IN HYBRID ZONES: A WINDOW ON TENSION ZONE MODELS, Evolution, vol.60, issue.11, pp.2789-806, 2008.
DOI : 10.1111/j.0014-3820.2006.tb01139.x

Z. Gompert, C. A. Et, and . Buerkle, Bayesian estimation of genomic clines, Molecular Ecology, vol.60, issue.10, pp.2111-2138, 2011.
DOI : 10.1111/j.0014-3820.2006.tb01139.x

Z. Gompert, C. A. Et, and . Buerkle, : Software for Bayesian estimation of genomic clines, Molecular Ecology Resources, vol.99, issue.6, pp.1168-76, 2012.
DOI : 10.1073/pnas.112324299

Z. Gompert, T. L. Parchman, and C. A. Buerkle, Genomics of isolation in hybrids, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.367, issue.1587, pp.439-50, 2012.
DOI : 10.1098/rstb.2011.0245

P. R. Grant, B. R. Et, and . Grant, Unpredictable Evolution in a 30-Year Study of Darwin's Finches, Science, vol.296, issue.5568, pp.707-718, 2002.
DOI : 10.1126/science.1070315

C. Grossen, S. S. Seneviratne, D. Croll, and D. E. Irwin, Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact, Molecular Ecology, vol.42, issue.17, pp.4247-4266
DOI : 10.1038/ng.546

R. N. Gutenkunst, R. D. Hernandez, S. H. Williamson, and C. D. Bustamante, Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data, PLoS Genetics, vol.81, issue.10, 2009.
DOI : 10.1371/journal.pgen.1000695.s001

U. Gyllensten, The genetic structure of fish: differences in the intraspecific distribution of biochemical genetic variation between marine, anadromous, and freshwater species, Journal of Fish Biology, vol.34, issue.6, pp.691-699, 1985.
DOI : 10.1016/0305-1978(81)90020-X

B. Harr, Genomic islands of differentiation between house mouse subspecies, Genome Research, vol.16, issue.6, pp.730-737, 2006.
DOI : 10.1101/gr.5045006

R. G. Harrison, Pattern and process in a narrow hybrid zone, Process in a Narrow Hybrid Zone, pp.337-349, 1986.
DOI : 10.1038/hdy.1986.55
URL : http://www.nature.com/hdy/journal/v56/n3/pdf/hdy198655a.pdf

R. G. Harrison, E. L. Et, and . Larson, Hybridization, Introgression, and the Nature of Species Boundaries, Journal of Heredity, vol.175, issue.S1, pp.795-809
DOI : 10.1534/genetics.106.064469

R. Harrison and . Gerald, Hybrid zones and the evolutionary process, 1993.

D. Hedgecock, A. I. Et, and . Pudovkin, Sweepstakes Reproductive Success in Highly Fecund Marine Fish and Shellfish: A Review and Commentary, Bulletin of Marine Science, vol.87, issue.4, pp.971-1002, 2011.
DOI : 10.5343/bms.2010.1051

D. K. Herrig, A. J. Modrick, E. Brud, and E. A. Llopart, SISTER SPECIES: EVIDENCE OF GENE FLOW IN NUCLEAR GENES DESPITE MITOCHONDRIAL DIFFERENTIATION, Evolution, vol.153, issue.Pt 3, pp.705-724
DOI : 10.1093/gbe/evq011

G. Hewitt, The genetic legacy of the Quaternary ice ages, Nature, vol.15, issue.6789, pp.907-920, 2000.
DOI : 10.1038/ng0197-99

J. Hey, R. Et, and . Nielsen, Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics, Proceedings of the National Academy of Sciences, vol.25, issue.2, pp.2785-90, 2007.
DOI : 10.1214/aoms/1177728725

D. A. Jackson, PROTEST: A PROcrustean Randomization TEST of community environment concordance, ??coscience, vol.2, issue.3, pp.297-303, 1995.
DOI : 10.1111/j.2044-8317.1983.tb00765.x

T. Jombart, adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics, vol.3, issue.11, pp.1403-1408, 2008.
DOI : 10.1093/oxfordjournals.jhered.a111573
URL : https://hal.archives-ouvertes.fr/hal-00428105

C. P. Klingenberg, M. Barluenga, and E. A. Meyer, Body shape variation in cichlid fishes of the Amphilophus citrinellus species complex, Biological Journal of the Linnean Society, vol.45, issue.3, pp.397-408, 2003.
DOI : 10.1111/j.1558-5646.1991.tb02662.x

A. S. Kondrashov and M. V. Mina, Sympatric speciation: when is it possible?, Biological Journal of the Linnean Society, vol.36, issue.346, pp.201-223, 1986.
DOI : 10.2307/2408092
URL : https://academic.oup.com/biolinnean/article-pdf/27/3/201/14066801/j.1095-8312.1986.tb01734.x.pdf

G. Kotoulas, F. Bonhomme, and E. P. Borsa, Genetic structure of the common sole Solea vulgaris at different geographic scales, Marine Biology, vol.13, issue.Suppl. A, pp.361-375, 1995.
DOI : 10.1007/978-3-642-93071-3_12

L. E. Kruuk, S. J. Baird, K. S. Gale, and N. H. Barton, «A comparison of multilocus clines maintained by environmental adaptation or by selection against hybrids, Genetics, vol.153, pp.1959-71, 1999.

B. Langmead, S. L. Et, and . Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-366, 2012.
DOI : 10.1093/bioinformatics/btp352
URL : http://europepmc.org/articles/pmc3322381?pdf=render

L. Moan, A. , P. Gagnaire, and E. F. Bonhomme, 2016. «Parallel genetic divergence among coastal? marine ecotype pairs of European anchovy explained by differential introgression after secondary contact, Molecular ecology

S. H. Martin, K. K. Dasmahapatra, N. J. Nadeau, C. Salazar, J. R. Walters et al., butterflies, Genome Research, vol.14, issue.11, pp.1817-1845, 2013.
DOI : 10.1126/science.1181661
URL : https://hal.archives-ouvertes.fr/hal-01190382

E. Mayr, Systematics and the origin of species, from the viewpoint of a zoologist, 1942.

E. Mayr, Animal species and evolution, 1963.
DOI : 10.4159/harvard.9780674865327

M. R. Miller, J. P. Dunham, A. Amores, W. A. Cresko, and E. A. Johnson, Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers, Genome Research, vol.17, issue.2, pp.240-248, 2007.
DOI : 10.1101/gr.5681207
URL : http://genome.cshlp.org/content/17/2/240.full.pdf

L. C. Moyle and E. B. Graham, Genome-Wide Associations Between Hybrid Sterility QTL and Marker Transmission Ratio Distortion, et Smbe Tri-National Young Investigators, pp.973-80, 2005.
DOI : 10.1093/molbev/msj112
URL : https://academic.oup.com/mbe/article-pdf/23/5/973/6235824/msj112.pdf

H. J. Muller, «Isolating mechanisms, evolution and temperature, » Biol. Symp, pp.71-125, 1942.

M. W. Nachman, B. A. Et, and . Payseur, 2012. «Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice.» Philos, Trans. R. Soc. Lond. B. Biol

. Sci, , pp.409-430

P. Nichols, M. J. Genner, C. Van-oosterhout, A. Smith, H. Parsons et al., Secondary contact seeds phenotypic novelty in cichlid fishes, «Secondary contact seeds phenotypic novelty in cichlid fishes, p.20142272, 2015.
DOI : 10.1111/j.1420-9101.2005.00932.x

E. E. Nielsen, H. Peter, D. Nielsen, M. M. Meldrup, and . Hansen, Genetic population structure of turbot (Scophthalmus maximus L.) supports the presence of multiple hybrid zones for marine fishes in the transition zone between the Baltic Sea and the North Sea, Molecular Ecology, vol.28, issue.3, pp.585-595, 2004.
DOI : 10.1006/jfbi.1994.1021

R. Nielsen, J. Et, and . Wakeley, «Distinguishing migration from isolation: a Markov chain Monte Carlo approach, Genetics, vol.158, pp.885-96, 2001.

M. A. Noor, S. M. Et, and . Bennett, Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species, Heredity, vol.145, issue.6, pp.439-483, 2009.
DOI : 10.1534/genetics.106.064469

P. Nosil, D. J. Funk, and E. D. Ortiz-barrientos, Divergent selection and heterogeneous genomic divergence, Molecular Ecology, vol.105, issue.3, pp.375-402, 2009.
DOI : 10.1111/j.0014-3820.2003.tb00595.x

H. A. Orr, «The population genetics of speciation: the evolution of hybrid incompatibilities, Genetics, vol.139, pp.1805-1818, 1995.

K. Ouanes, L. Bahri-sfar, O. K. Ben-hassine, and E. F. Bonhomme, Expanding hybrid zone between Solea aegyptiaca and Solea senegalensis: genetic evidence over two decades, Molecular Ecology, vol.14, issue.Suppl., pp.1717-1745, 2011.
DOI : 10.1046/j.1420-9101.2001.00335.x

S. R. 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

T. L. Parchman, Z. Gompert, M. J. Braun, R. T. Brumfield, D. B. Mcdonald et al., The genomic consequences of adaptive divergence and reproductive isolation between species of manakins, Molecular Ecology, vol.18, issue.12, pp.3304-3321, 2013.
DOI : 10.1111/j.1365-294X.2009.04381.x

K. J. Parsons, Y. H. Son, and R. C. Albertson, Hybridization Promotes Evolvability in African Cichlids: Connections Between Transgressive Segregation and Phenotypic Integration, Evolutionary Biology, vol.36, issue.Supplement, pp.306-315, 2011.
DOI : 10.1007/s11692-008-9034-7

T. Patarnello, F. A. Volckaert, and R. Castilho, Pillars of Hercules: is the Atlantic-Mediterranean transition a phylogeographical break?, Molecular Ecology, vol.122, issue.6, pp.4426-4444, 2007.
DOI : 10.1016/0031-0182(95)00091-7

P. R. Peres-neto and D. A. Jackson, How well do multivariate data sets match? The advantages of a Procrustean superimposition approach over the Mantel test, Oecologia, vol.129, issue.2, pp.169-178, 2001.
DOI : 10.1007/s004420100720

J. Pialek and N. H. Barton, «The spread of an advantageous allele across a barrier: the effects of random drift and selection against heterozygotes, Genetics, vol.145, pp.493-504, 1997.

D. C. Presgraves, The molecular evolutionary basis of species formation, Nature Reviews Genetics, vol.55, issue.3, pp.175-80, 2010.
DOI : 10.1111/j.0014-3820.2001.tb00628.x

J. C. Quéro, M. Desoutter, and E. F. Lagardère, «Soleidae.» Fishes of the North-eastern Atlantic and the Mediterranean, pp.1308-1324, 1986.

A. Raj, M. Stephens, and J. K. Pritchard, fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets, Genetics, vol.197, issue.2, pp.573-89, 2014.
DOI : 10.1534/genetics.114.164350

V. Ravigné, A. Barberousse, N. Bierne, J. Britton-davidian, P. Capy et al., , 2010.

L. H. Rieseberg, Chromosomal rearrangements and speciation, Trends in Ecology & Evolution, vol.16, issue.7, pp.351-358, 2001.
DOI : 10.1016/S0169-5347(01)02187-5

L. H. Rieseberg, A. Widmer, A. M. Arntz, and J. M. Burke, The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.358, issue.1434, pp.1141-1148, 2003.
DOI : 10.1098/rstb.2003.1283

L. H. Rieseberg and J. H. Willis, Plant Speciation, Science, vol.103, issue.27, pp.910-914, 2007.
DOI : 10.1073/pnas.0601928103

L. H. Rieseberg, J. Whitton, and E. K. Gardner, «Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species, Genetics, vol.152, pp.713-727, 1999.

L. H. Rieseberg, M. A. Archer, and R. K. Wayne, Transgressive segregation, adaptation and speciation, Heredity, vol.118, issue.4, pp.363-72, 1999.
DOI : 10.2135/cropsci1994.0011183X003400030015x

J. M. Roessig, C. M. Woodley, J. J. Cech, and L. J. Hansen, Effects of global climate change on marine and estuarine fishes and fisheries, Reviews in Fish Biology and Fisheries, vol.144, issue.6, pp.251-275, 2004.
DOI : 10.1034/j.1600-0870.1998.00010.x

F. J. Rohlf, «tpsDig, version 2.10.» Department of Ecology and Evolution, 2006.

J. L. Rolland, F. Bonhomme, F. Lagardere, M. Hassan, and E. B. Guinand, Population structure of the common sole (Solea solea) in the Northeastern Atlantic and the Mediterranean Sea: revisiting the divide with EPIC markers, Marine Biology, vol.13, issue.Suppl. 2, pp.327-341, 2007.
DOI : 10.1111/j.1469-1809.1949.tb02451.x

C. Roux, G. Tsagkogeorga, N. Bierne, and E. N. Galtier, Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species, Molecular Biology and Evolution, vol.19, issue.21, pp.1574-87, 2013.
DOI : 10.1111/j.1365-294X.2010.04837.x

S. Schlager and G. Jefferis, , 2015.

J. X. She, M. Autem, G. Kotulas, N. Pasteur, and E. F. Bonhomme, Multivariate analysis of genetic exchanges between Solea aegyptiaca and Solea senegalensis (Teleosts, Soleidae), Biological Journal of the Linnean Society, vol.305, issue.3, pp.357-371, 1987.
DOI : 10.5962/bhl.part.5286

C. Smadja, J. Galindo, and E. R. Butlin, Hitching a lift on the road to speciation, Molecular Ecology, vol.175, issue.19, pp.4177-80, 2008.
DOI : 10.1111/j.1365-294X.2008.03917.x
URL : https://hal.archives-ouvertes.fr/hal-01945570

J. M. Smith, J. Et, and . Haigh, The hitch-hiking effect of a favourable gene, Genetical Research, vol.19, issue.01, pp.23-35, 1974.
DOI : 10.1038/2191114a0

J. M. Sobel, G. F. Chen, L. R. Watt, and D. W. Schemske, THE BIOLOGY OF SPECIATION, Evolution, vol.276, issue.2, pp.295-315, 2010.
DOI : 10.1111/j.0014-3820.2000.tb00111.x

V. Sousa, J. Et, and . Hey, Understanding the origin of species with genome-scale data: modelling gene flow, Nature Reviews Genetics, vol.154, issue.6, pp.404-418, 2013.
DOI : 10.1093/bioinformatics/18.2.337

S. Stankowski, J. M. Sobel, and M. A. Streisfeld, «Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower, Molecular ecology, 2016.

R. B. Stelkens, C. Schmid, O. Selz, and E. O. Seehausen, Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish, BMC Evolutionary Biology, vol.9, issue.1, p.283, 2009.
DOI : 10.1186/1471-2148-9-283

K. N. Stölting, R. Nipper, D. Lindtke, C. Caseys, S. Waeber et al., Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species, Molecular Ecology, vol.12, issue.3, pp.842-855, 2013.
DOI : 10.1046/j.1365-294X.2003.01773.x

S. A. Taylor, R. L. Curry, T. A. White, V. Ferretti, and E. I. Lovette, Spatiotemporally consistent genomic signatures of reproductive isolation in a moving hybrid zone, Evolution, vol.14, issue.11, pp.3066-81
DOI : 10.1046/j.1420-9101.2001.00335.x

K. C. Teeter, L. M. Thibodeau, Z. Gompert, C. A. Buerkle, M. W. Nachman et al., THE VARIABLE GENOMIC ARCHITECTURE OF ISOLATION BETWEEN HYBRIDIZING SPECIES OF HOUSE MICE, Evolution, vol.60, issue.2, pp.472-485, 2010.
DOI : 10.1111/j.0014-3820.2006.tb01139.x

M. Tine, H. Kuhl, P. A. Gagnaire, B. Louro, E. Desmarais et al., European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation, Nature Communications, vol.28, issue.1, p.5770, 2014.
DOI : 10.1093/bioinformatics/bts606
URL : http://www.nature.com/articles/ncomms6770.pdf

M. Turelli and H. A. Orr, «The dominance theory of Haldane's rule, Genetics, vol.140, pp.389-402, 1995.

J. R. Turner, «Why does the genotype not congeal?, pp.645-656, 1967.
DOI : 10.2307/2406761

J. Vachon, F. Chapleau, and M. Desoutter-meniger, «Révision taxinomique du genre Solea et réhabilitation du genre Barnardichthys (Soleidae; Pleuronectiformes), » Cybium, vol.32, pp.9-26, 2008.

S. Via, J. Et, and . West, The genetic mosaic suggests a new role for hitchhiking in ecological speciation, Molecular Ecology, vol.175, issue.19, pp.4334-4379, 2008.
DOI : 10.1111/j.0014-3820.2000.tb00707.x

J. Wakeley, J. Et, and . Hey, «Estimating ancestral population parameters, Genetics, vol.145, pp.847-55, 1997.

R. S. Waples, Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species, Journal of Heredity, vol.89, issue.5, pp.438-450, 1998.
DOI : 10.1093/jhered/89.5.438

R. D. Ward, M. Woodwark, and D. O. Skibinski, A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes, Journal of Fish Biology, vol.32, issue.2, pp.213-232, 1994.
DOI : 10.1007/BF00004955

P. J. Whitehead, M. L. Bauchot, J. C. Hureau, J. Nielson, and E. E. Tortonese, «Fishes of the North-eastern Atlantic and the Mediterranean, 1986.

J. D. Wilson, D. J. Schmidt, and J. M. Hughes, ), «Movement of a Hybrid Zone Between Lineages of the Australian Glass Shrimp, pp.413-422, 2016.
DOI : 10.3732/ajb.1400201

M. Yúfera, G. Parra, R. Santiago, and E. M. Carrascosa, Growth, carbon, nitrogen and caloric content of Solea senegalensis (Pisces: Soleidae) from egg fertilization to metamorphosis, Marine Biology, vol.134, issue.1, pp.43-49, 1999.
DOI : 10.1007/s002270050523

M. Zelditch, Geometric morphometrics for biologists : a primer. Amsterdam, 2004.

J. A. Addison, B. S. Ort, K. A. Mesa, and G. H. Pogson, ): a comparison of allozymes, nuclear DNA markers, and mitochondrial DNA sequences, Molecular Ecology, vol.25, issue.19, pp.4222-4232, 2008.
DOI : 10.1093/oxfordjournals.molbev.a025673

F. W. Allendorf, P. A. Hohenlohe, and G. Luikart, Genomics and the future of conservation genetics, Nature Reviews Genetics, vol.106, issue.10, pp.697-709, 2010.
DOI : 10.1111/j.0014-3820.2003.tb00580.x

G. R. Almany, M. L. Berumen, S. R. Thorrold, S. Planes, and G. P. Jones, Local Replenishment of Coral Reef Fish Populations in a Marine Reserve, Science, vol.316, issue.5825, pp.742-744, 2007.
DOI : 10.1126/science.1140597
URL : https://hal.archives-ouvertes.fr/hal-00170715

G. R. Almany, R. J. Hamilton, M. Bode, M. Matawai, T. Potuku et al., Dispersal of Grouper Larvae Drives Local Resource Sharing in a Coral Reef Fishery, Current Biology, vol.23, issue.7, pp.626-630, 2013.
DOI : 10.1016/j.cub.2013.03.006

I. C. Ansmann, G. J. Parra, J. M. Lanyon, and J. M. Seddon, Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia, Molecular Ecology, vol.198, issue.18, pp.4472-4485, 2012.
DOI : 10.1126/science.198.4318.755

D. Aurelle and J. Ledoux, Interplay between isolation by distance and genetic clusters in the red coral Corallium rubrum: insights from simulated and empirical data, Conservation Genetics, vol.61, issue.5, pp.705-716, 2013.
DOI : 10.1093/sysbio/sys048

N. H. Barton, The dynamics of hybrid zones, Heredity, vol.43, issue.3, pp.341-359, 1979.
DOI : 10.1038/hdy.1979.87

N. H. Barton, Gene flow past a cline, Heredity, vol.43, issue.3, pp.333-339, 1979.
DOI : 10.1038/hdy.1979.86

N. H. Barton, MULTILOCUS CLINES, Evolution, vol.34, issue.3, pp.454-471, 1983.
DOI : 10.2307/2407990

N. H. Barton and K. S. Gale, Genetic analysis of hybrid zones, Hybrid Zones and the Evolutionary Process, pp.13-45, 1993.

A. O. Bergland, R. Tobler, J. Gonzalez, P. Schmidt, and D. Petrov, Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster, 2015.
DOI : 10.1101/009084

A. Berry and M. Kreitman, Molecular analysis of an allozyme cline: alcohol dehydrogenase in Drosophila melanogaster on the east coast of North America, Genetics, vol.134, pp.869-893, 1993.

N. Bierne, THE DISTINCTIVE FOOTPRINTS OF LOCAL HITCHHIKING IN A VARIED ENVIRONMENT AND GLOBAL HITCHHIKING IN A SUBDIVIDED POPULATION, Evolution, vol.326, issue.11, pp.3254-3272, 2010.
DOI : 10.1111/j.0014-3820.2001.tb00656.x

N. Bierne, J. Welch, E. Loire, F. Bonhomme, and P. David, The coupling hypothesis: why genome scans may fail to map local adaptation genes, Molecular Ecology, vol.17, issue.Suppl 1, pp.2044-2072, 2011.
DOI : 10.1111/j.1365-294X.2008.03755.x

N. Bierne, D. Roze, and J. J. Welch, outliers sometimes so frequent?, Molecular Ecology, vol.17, issue.8, pp.2061-2064, 2013.
DOI : 10.1111/j.1365-294X.2008.03712.x

C. Blair, D. E. Weigel, M. Balazik, A. T. Keeley, F. M. Walker et al., A simulation-based evaluation of methods for inferring linear barriers to gene flow, Molecular Ecology Resources, vol.7, issue.5, pp.822-833, 2012.
DOI : 10.1186/1471-2105-7-317

M. Bonhomme, C. Chevalet, B. Servin, S. Boitard, J. Abdallah et al., Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended, Genetics, vol.186, issue.1, pp.241-262, 2010.
DOI : 10.1534/genetics.110.117275
URL : https://hal.archives-ouvertes.fr/hal-00842515

I. R. Bradbury, S. Hubert, B. Higgins, T. Borza, S. Bowman et al., Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature, Proceedings of the Royal Society B: Biological Sciences, vol.17, issue.5890, pp.3725-3734, 2010.
DOI : 10.1126/science.1160852

T. Broquet and E. J. Petit, Molecular Estimation of Dispersal for Ecology and Population Genetics, Annual Review of Ecology, Evolution, and Systematics, vol.40, issue.1, pp.193-216, 2009.
DOI : 10.1146/annurev.ecolsys.110308.120324
URL : https://hal.archives-ouvertes.fr/hal-00448683

T. Broquet, J. Yearsley, A. H. Hirzel, J. Goudet, and N. Perrin, Inferring recent migration rates from individual genotypes, Molecular Ecology, vol.16, issue.6, pp.1048-1060, 2009.
DOI : 10.1017/CBO9780511808999

B. Charlesworth, M. Morgan, and D. Charlesworth, The effect of deleterious mutations on neutral molecular variation, Genetics, vol.134, pp.1289-1303, 1993.

B. Charlesworth, M. Nordborg, and D. Charlesworth, The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations, Genetical Research, vol.70, issue.2, pp.155-174, 1997.
DOI : 10.1017/S0016672397002954

M. R. Christie, B. N. Tissot, M. A. Albins, J. P. Beets, Y. Jia et al., Larval Connectivity in an Effective Network of Marine Protected Areas, PLoS ONE, vol.32, issue.12, p.15715, 2010.
DOI : 10.1371/journal.pone.0015715.s002

J. Clobert, M. Baguette, T. G. Benton, J. M. Bullock, and S. Ducatez, Dispersal Ecology and Evolution, 2012.
DOI : 10.1093/acprof:oso/9780199608898.001.0001

G. J. Colbeck, J. Turgeon, P. Sirois, and J. J. Dodson, Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus), Molecular Ecology, vol.8, issue.9, pp.1976-1987, 2011.
DOI : 10.1046/j.1365-294x.1999.00620.x

J. Corander, P. Waldmann, and M. J. , Bayesian analysis of genetic differentiation between Populations, Genetics, vol.163, pp.367-374, 2003.

C. I. Cullingham, J. E. Cooke, and D. W. Coltman, ), Genome, vol.30, issue.10, pp.577-585, 2013.
DOI : 10.1111/mec.12199

J. W. Davey, P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen et al., Genome-wide genetic marker discovery and genotyping using next-generation sequencing, Nature Reviews Genetics, vol.464, issue.7, pp.499-510, 2011.
DOI : 10.1038/nature08832

D. Mita, S. , A. Thuillet, L. Gay, N. Ahmadi et al., Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations, Molecular Ecology, vol.38, issue.5, pp.1383-1399, 2013.
DOI : 10.2307/2408641
URL : https://hal.archives-ouvertes.fr/hal-01268008

D. Villemereuil, P. , E. Frichot, E. Bazin, O. Franc et al., Genome scan methods against more complex models: when and how much should we trust them?, Molecular Ecology, vol.65, issue.8, pp.2006-2019, 2014.
DOI : 10.1111/j.1558-5646.2011.01269.x
URL : https://hal.archives-ouvertes.fr/hal-02004812

J. A. Dewoody and J. C. Avise, Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals, Journal of Fish Biology, vol.4, issue.3, pp.461-473, 2000.
DOI : 10.1046/j.1420-9101.1999.00006.x

N. Duforet-frebourg, E. Bazin, and M. G. Blum, Genome Scans for Detecting Footprints of Local Adaptation Using a Bayesian Factor Model, Molecular Biology and Evolution, vol.329, issue.9, pp.2483-2495, 2014.
DOI : 10.1126/science.1190371
URL : https://hal.archives-ouvertes.fr/hal-01053023

C. F. Duggins, A. A. Karlin, T. A. Mousseau, and K. G. Relyea, Analysis of a hybrid zone in Fundulus majalis in a northeastern Florida ecotone, Heredity, vol.74, issue.2, pp.117-128, 1995.
DOI : 10.1038/hdy.1995.18

E. Durand, F. Jay, O. E. Gaggiotti, and O. Franc, Spatial Inference of Admixture Proportions and Secondary Contact Zones, Molecular Biology and Evolution, vol.38, issue.2, pp.1963-1973, 2009.
DOI : 10.1038/ng1702

J. A. Endler, Geographic Variation, Speciation, and Clines, 1977.

L. Excoffier, T. Hofer, and M. Foll, Detecting loci under selection in a hierarchically structured population, Heredity, vol.15, issue.4, pp.285-298, 2009.
DOI : 10.1534/genetics.106.061432

D. K. Fabian, M. Kapun, V. Nolte, R. Kofler, P. S. Schmidt et al., from North America, Molecular Ecology, vol.186, issue.19, pp.4748-4769, 2012.
DOI : 10.1534/genetics.110.117366

M. F. Faure, P. David, F. Bonhomme, and N. Bierne, Genetic hitchhiking in a subdivided population of Mytilus edulis, BMC Evolutionary Biology, vol.8, issue.1, p.164, 2008.
DOI : 10.1186/1471-2148-8-164
URL : https://hal.archives-ouvertes.fr/halsde-00475073

M. Foll, O. E. Gaggiotti, J. T. Daub, and A. Vatsiou, Wide- spreadsignalsofconvergentadaptationtohighaltitudeinAsiaandAmerica, pp.394-407

Y. Fourcade, A. Chaput-bardy, J. Secondi, C. Fleurant, and C. Lemaire, Is local selection so widespread in river organisms? Fractal geometry of river networks leads to high bias in outlier detection, Molecular Ecology, vol.15, issue.8, pp.2065-2073, 2013.
DOI : 10.1111/j.1469-1809.1949.tb02451.x
URL : https://hal.archives-ouvertes.fr/hal-00812551

C. Fra?-isse, C. Roux, J. J. Welch, and N. Bierne, Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?, Genetics, vol.197, issue.3, pp.939-951, 2014.
DOI : 10.1534/genetics.114.161380

C. Fra?-isse, K. Belkhir, J. J. Welch, and N. Bierne, Local inter-species introgression is the main cause of outlying levels of intra-specific differentiation in mussels, Molecular Ecology, 2015.

O. Franc-ßois and E. Durand, Spatially explicit Bayesian clustering models in population genetics, Molecular Ecology Resources, vol.24, issue.5, pp.773-784, 2010.
DOI : 10.1111/j.1469-1809.1949.tb02451.x

W. C. Funk, J. K. Mckay, P. A. Hohenlohe, and F. W. Allendorf, Harnessing genomics for delineating conservation units, Trends in Ecology & Evolution, vol.27, issue.9, pp.489-496, 2012.
DOI : 10.1016/j.tree.2012.05.012

O. E. Gaggiotti, F. Jones, W. M. Lee, W. Amos, J. Harwood et al., Patterns of colonization in a metapopulation of grey seals, Nature, vol.21, issue.6879, pp.424-427, 2002.
DOI : 10.1063/1.1699114

P. Gagnaire, Y. Minegishi, S. Zenboudji, P. Valade, J. Aoyama et al., WITHIN-POPULATION STRUCTURE HIGHLIGHTED BY DIFFERENTIAL INTROGRESSION ACROSS SEMIPERMEABLE BARRIERS TO GENE FLOW IN ANGUILLA MARMORATA, Evolution, vol.8, issue.12, pp.3413-3427, 2011.
DOI : 10.1046/j.1365-294x.1999.00620.x

P. Gagnaire, E. Normandeau, C. C^-ot-e, M. M. Hansen, and L. Bernatchez, ), Genetics, vol.190, issue.2, pp.725-736, 2012.
DOI : 10.1534/genetics.111.134825

H. Gao, S. Williamson, and C. D. Bustamante, A Marko Chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data, Genetics, vol.76, pp.1635-1651, 2007.

M. R. Gilg and T. J. Hilbish, THE GEOGRAPHY OF MARINE LARVAL DISPERSAL: COUPLING GENETICS WITH FINE-SCALE PHYSICAL OCEANOGRAPHY, Ecology, vol.84, issue.11, pp.2989-2998, 2003.
DOI : 10.4319/lo.1998.43.7.1710

Z. Gompert and C. A. Buerkle, Analyses of genetic ancestry enable key insights for molecular ecology, Molecular Ecology, vol.9, issue.21, pp.5278-5294, 2013.
DOI : 10.1371/journal.pgen.1003264

M. A. Gore, J. M. Chia, R. J. Elshire, Q. Sun, E. S. Ersoz et al., A First-Generation Haplotype Map of Maize, Science, vol.5, issue.11, pp.1115-1117, 2009.
DOI : 10.1371/journal.pgen.1000743

C. C. Gosset and N. Bierne, outlier loci within a mussel species, Journal of Evolutionary Biology, vol.8, issue.1, pp.14-26, 2013.
DOI : 10.1046/j.1365-294x.1999.00620.x

C. C. Gosset, J. D. Nascimento, M. T. Aug, and N. Bierne, Molecular Ecology, vol.8, issue.12, pp.3000-3012, 2014.
DOI : 10.1046/j.1365-294x.1999.00620.x

S. Gravel, Population Genetics Models of Local Ancestry, Genetics, vol.191, issue.2, pp.607-619, 2012.
DOI : 10.1534/genetics.112.139808

D. Hedgecock, P. H. Barber, and S. , Genetic Approaches to Measuring Connectivity, Oceanography, vol.20, issue.3, pp.70-79, 2007.
DOI : 10.5670/oceanog.2007.30

M. E. Hellberg, Gene Flow and Isolation among Populations of Marine Animals, Annual Review of Ecology, Evolution, and Systematics, vol.40, issue.1, pp.291-310, 2009.
DOI : 10.1146/annurev.ecolsys.110308.120223

J. Hemmer-hansen, E. E. Nielsen, N. O. Therkildsen, M. I. Taylor, R. Ogden et al., A genomic island linked to ecotype divergence in Atlantic cod, Molecular Ecology, vol.65, issue.Suppl 1, pp.2653-2667, 2013.
DOI : 10.1111/j.1558-5646.2011.01269.x

G. P. Jones, S. Planes, and S. R. Thorrold, Coral Reef Fish Larvae Settle Close to Home, Current Biology, vol.15, issue.14, pp.1314-1318, 2005.
DOI : 10.1016/j.cub.2005.06.061

L. O. Jost, and its relatives do not measure differentiation, Molecular Ecology, vol.15, issue.18, pp.4015-4026, 2008.
DOI : 10.1111/j.1469-1809.1949.tb02451.x

R. Jovelin, J. S. Comstock, A. D. Cutter, and P. C. Phillips, G3: Genes|Genomes|Genetics, vol.4, issue.6, pp.1123-1133, 2014.
DOI : 10.1534/g3.114.010629

B. O. Karlsen, K. Klingan, A. Emblem, T. E. Jørgensen, A. Jueterbock et al., Genomic divergence between the migratory and stationary ecotypes of Atlantic cod, Molecular Ecology, vol.7, issue.20, pp.5098-5111, 2013.
DOI : 10.1371/journal.pone.0051540

R. K. Koehn, R. I. Newell, and F. Immermann, Maintenance of an aminopeptidase allele frequency cline by natural selection., Proceedings of the National Academy of Sciences, vol.77, issue.9, pp.5385-5389, 1980.
DOI : 10.1073/pnas.77.9.5385

L. E. Kruuk, S. J. Baird, K. S. Gale, and N. H. Barton, A comparison of multilocus clines maintained by environmental adaptation or by selection against hybrids, Genetics, vol.153, pp.1959-1971, 1999.

S. Lamichhaney, A. M. Barrio, N. Rafati, G. Sundstr?-om, C. Rubin et al., Population-scale sequencing reveals 16 © 2015 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd Marine connectivity in the genomic era Gagnaire et al. genetic differentiation due to local adaptation in Atlantic herring, Proceedings of the National Academy of Sciences, pp.19345-19350, 2012.

C. H. Langley, K. Stevens, C. Cardeno, Y. C. Lee, D. R. Schrider et al., Genomic Variation in Natural Populations of Drosophila melanogaster, Genetics, vol.192, issue.2, pp.533-598, 2012.
DOI : 10.1534/genetics.112.142018

H. H. Lassen and F. J. Turano, Clinal variation and heterozygote deficit at the lap-locus in Mytilus edulis, Marine Biology, vol.27, issue.3, pp.245-254, 1978.
DOI : 10.1007/BF00391137

E. K. Latch, G. Dharmarajan, J. C. Glaubitz, and O. E. Rhodes-jr, Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation, Conservation Genetics, vol.18, issue.2, pp.295-302, 2006.
DOI : 10.1093/oxfordjournals.molbev.a003956

L. Corre, V. , and A. , The genetic differentiation at quantitative trait loci under local adaptation, Molecular Ecology, vol.65, issue.7, pp.1548-1566
DOI : 10.1111/j.1558-5646.2011.01269.x

J. B. Ledoux, J. Garrabou, O. Bianchimani, P. Drap, J. P. et al.,

. Aurelle, Fine-scale genetic structure and inferences on population biology in the threatened Mediterranean red coral, Corallium rubrum, Molecular Ecology, vol.19, pp.4204-4216, 2010.

T. Lenormand, T. Guillemaud, D. Bourguet, and M. Raymond, Evaluating gene flow using selected markers: a case study, Genetics, vol.149, pp.1383-1392, 1998.
URL : https://hal.archives-ouvertes.fr/halsde-00188542

H. Levene, Genetic Equilibrium When More Than One Ecological Niche is Available, The American Naturalist, vol.87, issue.836, pp.331-333, 1953.
DOI : 10.1086/281792

M. Liang and R. Nielsen, The Lengths of Admixture Tracts, Genetics, vol.197, issue.3, pp.953-967, 2014.
DOI : 10.1534/genetics.114.162362

M. T. Limborg, S. J. Helyar, M. De-bruyn, M. I. Taylor, E. E. Nielsen et al., ), Molecular Ecology, vol.65, issue.15, pp.3686-3703, 2012.
DOI : 10.1111/j.1558-5646.2011.01269.x

K. Lotterhos and M. Whitlock, outlier tests, Molecular Ecology, vol.65, issue.Suppl 1, pp.2178-2192, 2014.
DOI : 10.1111/j.1558-5646.2011.01269.x

W. H. Lowe and F. W. Allendorf, What can genetics tell us about population connectivity?, Molecular Ecology, vol.18, issue.15, pp.3038-3051, 2010.
DOI : 10.1111/j.1469-1809.1949.tb02451.x

G. Luikart, P. R. England, D. Tallmon, S. Jordan, and P. Taberlet, The power and promise of population genomics: from genotyping to genome typing, Nature Reviews Genetics, vol.6, issue.12, pp.981-994, 2003.
DOI : 10.1086/302574
URL : https://hal.archives-ouvertes.fr/halsde-00279787

V. Lukoschek and R. Shine, Sea snakes rarely venture far from home, Ecology and Evolution, vol.26, issue.Suppl. 1, pp.1113-1121, 2012.
DOI : 10.3354/meps08287
URL : https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.256

P. B. Marko and M. W. Hart, The complex analytical landscape of gene flow inference, Trends in Ecology & Evolution, vol.26, issue.9, pp.448-456, 2011.
DOI : 10.1016/j.tree.2011.05.007

M. Smith, J. , and J. Haigh, The hitch-hiking effect of a favourable gene, Genetical Research, vol.19, issue.01, pp.23-35, 1974.
DOI : 10.1038/2191114a0

M. R. Mccusker and P. Bentzen, Positive relationships between genetic diversity and abundance in fishes, Molecular Ecology, vol.39, issue.22, pp.4852-4862, 2010.
DOI : 10.1111/j.0014-3820.2001.tb00732.x

M. H. Van-der-meer, J. A. Hobbs, G. P. Jones, and L. Van-herwerden, Genetic Connectivity among and Self-Replenishment within Island Populations of a Restricted Range Subtropical Reef Fish, PLoS ONE, vol.58, issue.6, p.49660, 2012.
DOI : 10.1371/journal.pone.0049660.s005

P. G. Meirmans, The trouble with isolation by distance, Molecular Ecology, vol.28, issue.12, pp.2839-2846, 2012.
DOI : 10.1111/j.0030-1299.2004.12497.x

P. G. Meirmans and P. W. Hedrick, Assessing population structure: FST and related measures, Molecular Ecology Resources, vol.19, issue.1, pp.5-18, 2011.
DOI : 10.1111/j.0014-3820.2004.tb01728.x

K. Mokhtar-jama?-i, M. Pascual, J. B. Ledoux, R. Coma, J. P. et al., From global to local genetic structuring in the red gorgonian Paramuricea clavata: the interplay between oceanographic conditions and limited larval dispersal, Molecular Ecology, vol.11, issue.16, pp.3291-3305, 2011.
DOI : 10.1890/1051-0761(2001)011[1472:RGDIET]2.0.CO;2

M. C. Murray and M. P. Hare, Molecular Ecology, vol.14, issue.13, pp.4229-4242, 2006.
DOI : 10.1046/j.1420-9101.2001.00304.x

T. Nagylaki, Conditions for the existence of clines, Genetics, vol.80, pp.595-615, 1975.

S. R. Narum and J. E. Hess, outlier tests for SNP loci under selection, Molecular Ecology Resources, vol.3, pp.184-194, 2011.
DOI : 10.1371/journal.pone.0003392

E. E. Nielsen, J. Hemmer-hansenn, P. F. Larsen, and D. Bekkevold, Population genomics of marine fishes: identifying adaptive variation in space and time, Molecular Ecology, vol.89, issue.Suppl. C, pp.3128-3150, 2009.
DOI : 10.1186/1479-7364-1-3-218

E. E. Nielsen, A. Cariani, E. Mac-aoidh, G. E. Maes, I. Milano et al., Gene-associated markers provide tools for tackling illegal fishing and false eco-certification, Nature Communications, vol.86, issue.1, p.851, 2012.
DOI : 10.1093/oxfordjournals.jhered.a111573

J. Novembre, T. Johnson, K. Bryc, Z. Kutalik, A. R. Boyko et al., Genes mirror geography within Europe. Nature, vol.456, pp.98-101, 2008.

O. Connor, T. D. , and W. Fu,

J. C. Turner, B. Mychaleckyj, and . Logsdon, Rare variation facilitates inferences of fine-scale population structure in humans, Molecular Biology and Evolution, vol.32, pp.653-660, 2014.

D. Paetkau, R. Slade, M. Burden, and A. Estoup, Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power, Molecular Ecology, vol.16, issue.1, pp.55-65, 2004.
DOI : 10.1016/B978-012323445-2/50005-5

P. F. Palamara and I. Pe-'er, Inference of historical migration rates via haplotype sharing, Bioinformatics, vol.131, issue.2, pp.180-188, 2013.
DOI : 10.1007/s00439-011-1072-z

S. R. Palumbi, POPULATION GENETICS, DEMOGRAPHIC CONNECTIVITY, AND THE DESIGN OF MARINE RESERVES, Ecological Applications, vol.13, issue.sp1, pp.146-158, 2003.
DOI : 10.1890/1051-0761(2003)013[0146:PGDCAT]2.0.CO;2

N. Patterson, A. L. Price, and D. Reich, Population Structure and Eigenanalysis, PLoS Genetics, vol.15, issue.12, p.190, 2006.
DOI : 1088-9051(2005)015[1576:CACSOH]2.0.CO;2

C. Perrier, R. Guyomard, J. Bagliniere, and G. Evanno, Determinants of hierarchical genetic structure in Atlantic salmon populations: environmental factors vs. anthropogenic influences, Molecular Ecology, vol.142, issue.20, pp.4231-4245, 2011.
DOI : 10.1016/j.biocon.2009.05.034

M. L. Pinsky, H. R. Montes-jr, and S. R. Palumbi, USING ISOLATION BY DISTANCE AND EFFECTIVE DENSITY TO ESTIMATE DISPERSAL SCALES IN ANEMONEFISH, Evolution, vol.38, issue.9, pp.2688-2700, 2010.
DOI : 10.1111/j.0014-3820.2005.tb01809.x

S. Planes, G. P. Jones, and S. R. Thorrold, Larval dispersal connects fish populations in a network of marine protected areas, Proceedings of the National Academy of Sciences, vol.63, issue.22, pp.5693-5697, 2009.
DOI : 10.1139/f06-048
URL : https://hal.archives-ouvertes.fr/halsde-00431334

G. H. Pogson, C. T. Taggart, K. A. Mesa, and R. G. Boutilier, ISOLATION BY DISTANCE IN THE ATLANTIC COD, GADUS MORHUA, AT LARGE AND SMALL GEOGRAPHIC SCALES, Evolution, vol.28, issue.1, pp.131-146, 2001.
DOI : 10.1046/j.1365-2540.1999.00496.x

J. E. Pool and R. Nielsen, Inference of Historical Changes in Migration Rate From the Lengths of Migrant Tracts, Genetics, vol.181, issue.2, pp.711-719, 2009.
DOI : 10.1534/genetics.108.098095

A. Popescu, A. L. Harper, M. Trick, I. Bancroft, and K. T. Huber, A novel and fast approach for population structure inference using kernel-PCA and optimization (PSIKO), Genetics, vol.114, p.171314, 2014.

D. A. Powers and A. R. Place, Biochemical genetics of Fundulus heteroclitus (L.). I. Temporal and spatial variation in gene frequencies of Ldh-B, Mdh-A, Gpi-B, and Pgm-A, Biochemical Genetics, vol.175, issue.5-6, pp.593-607, 1978.
DOI : 10.1016/B978-0-12-472704-5.50011-2

J. K. Pritchard and A. Di-rienzo, Adaptation ??? not by sweeps alone, Nature Reviews Genetics, vol.183, issue.10, pp.665-667, 2010.
DOI : 10.1038/nrg2880

. Gagnaire, Marine connectivity in the genomic era
URL : https://hal.archives-ouvertes.fr/hal-01187735

J. K. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using multilocus genotype data, Genetics, vol.155, pp.945-959, 2000.

O. Puebla, E. Bermingham, and F. Guichard, Estimating dispersal from genetic isolation by distance in a coral reef fish (Hypoplectrus puella), Ecology, vol.15, issue.11, pp.3087-3098, 2009.
DOI : 10.1111/j.1469-1809.1949.tb02451.x

O. Puebla, E. Bermingham, and W. O. Mcmillan, On the spatial scale of dispersal in coral reef fishes, Molecular Ecology, vol.42, issue.23, pp.5675-5688, 2012.
DOI : 10.1017/S003060530800046X

A. Raj, M. Stephens, and J. K. Pritchard, Variational inference of population structure in large SNP datasets, Genetics, vol.114, p.164350, 2014.
DOI : 10.1101/001073

P. Ralph and G. Coop, Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?, Genetics, vol.186, issue.2, pp.647-668, 2010.
DOI : 10.1534/genetics.110.119594

M. Roesti, A. P. Hendry, W. Salzburger, and D. Berner, Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs, Molecular Ecology, vol.14, issue.12, pp.2852-2862, 2012.
DOI : 10.1046/j.1420-9101.2001.00351.x

M. Roesti, S. Gavrilets, A. P. Hendry, W. Salzburger, and D. Berner, The genomic signature of parallel adaptation from shared genetic variation, Molecular Ecology, vol.14, issue.16, pp.3944-3956, 2014.
DOI : 10.1046/j.1420-9101.2001.00335.x

C. G. Rose, K. T. Paynter, and M. P. Hare, Isolation by Distance in the Eastern Oyster, Crassostrea virginica, in Chesapeake Bay, Journal of Heredity, vol.97, issue.2, pp.158-170, 2006.
DOI : 10.1046/j.1365-294x.1998.00477.x

F. Rousset, Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance, Genetics, vol.145, pp.1219-1228, 1997.

F. Rousset, Genetic differentiation between individuals, Journal of Evolutionary Biology, vol.28, issue.1, pp.58-62, 2000.
DOI : 10.1111/j.1558-5646.1991.tb04361.x

F. Rousset, Genetic Structure and Selection in Subdivided Populations, 2004.

P. Saenz-agudelo, G. P. Jones, S. R. Thorrold, and S. Planes, Connectivity dominates larval replenishment in a coastal reef fish metapopulation, Proceedings of the Royal Society B: Biological Sciences, vol.28, issue.4, pp.2954-2961, 2011.
DOI : 10.1007/s00338-008-0463-7
URL : https://hal.archives-ouvertes.fr/hal-00655369

P. S. Schmidt, E. A. Serr~-ao, G. A. Pearson, C. Riginos, P. D. Rawson et al., ECOLOGICAL GENETICS IN THE NORTH ATLANTIC: ENVIRONMENTAL GRADIENTS AND ADAPTATION AT SPECIFIC LOCI, Ecology, vol.103, issue.sp11, pp.91-107, 2008.
DOI : 10.1046/j.1365-2540.2000.00677.x

D. R. Schrider, F. K. Mendes, M. W. Hahn, and A. D. Kern, Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps, Genetics, vol.200, issue.1, pp.267-284, 2015.
DOI : 10.1534/genetics.115.174912

M. K. Schwartz and K. S. Mckelvey, Why sampling scheme matters: the effect of sampling scheme on landscape genetic results, Conservation Genetics, vol.62, issue.2, pp.441-452, 2009.
DOI : 10.1371/journal.pgen.0010070

K. A. Selkoe and R. J. Toonen, Marine connectivity: a new look at pelagic larval duration and genetic metrics of dispersal, Marine Ecology Progress Series, vol.436, pp.291-305, 2011.
DOI : 10.3354/meps09238

K. A. Selkoe, J. R. Watson, C. White, T. B. Horin, M. Iacchei et al., Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species, Molecular Ecology, vol.30, issue.17, pp.3708-3726, 2010.
DOI : 10.1111/j.0014-3820.2004.tb00466.x

M. Slatkin, Gene flow and selection in a cline, Genetics, vol.75, pp.733-756, 1973.

E. E. Sotka and S. R. Palumbi, THE USE OF GENETIC CLINES TO ESTIMATE DISPERSAL DISTANCES OF MARINE LARVAE, Ecology, vol.87, issue.5, pp.1094-1103, 2006.
DOI : 10.2307/2405519

E. E. Sotka, J. P. Wares, J. A. Barth, R. K. Grosberg, and S. R. Palumbi, Strong genetic clines and geographical variation in gene flow in the rocky intertidal barnacle Balanus glandula, Molecular Ecology, vol.40, issue.8, pp.2143-2156, 2004.
DOI : 10.1111/j.0014-3820.2001.tb01294.x

J. Stapley, J. Reger, P. G. Feulner, C. Smadja, J. Galindo et al., Adaptation genomics: the next generation, Trends in Ecology & Evolution, vol.25, issue.12, pp.705-712, 2010.
DOI : 10.1016/j.tree.2010.09.002
URL : https://hal.archives-ouvertes.fr/hal-01945554

J. F. Storz, INVITED REVIEW: Using genome scans of DNA polymorphism to infer adaptive population divergence, Molecular Ecology, vol.15, issue.113, pp.671-688, 2005.
DOI : 10.1111/j.1469-1809.1949.tb02451.x

M. P. Stumpf and G. A. Mcvean, Estimating recombination rates from population-genetic data, Nature Reviews Genetics, vol.7, issue.12, pp.959-968, 2003.
DOI : 10.1016/0040-5809(75)90020-9

S. E. Swearer, J. S. Shima, M. E. Hellberg, S. R. Thorrold, G. P. Jones et al., Evidence of self-recruitment in demersal marine populations, Bulletin of Marine Science, vol.70, pp.251-271, 2002.

J. M. Szymura and N. H. Barton, Genetic analysis of a hybrid zone between the fire-bellied toads, Bombina bombina and B. variegata, Near Cracow in Southern Poland, Evolution, vol.40, pp.1141-1159, 1986.

M. Tine, H. Kuhl, P. Gagnaire, B. Louro, E. Desmarais et al., European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation, Nature Communications, vol.28, issue.1, p.5770, 2014.
DOI : 10.1093/bioinformatics/bts606
URL : https://hal.archives-ouvertes.fr/hal-01922671

J. N. Underwood, L. D. Smith, M. J. Van-oppen, and J. P. Gilmour, Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching, Molecular Ecology, vol.25, issue.Suppl., pp.771-784, 2007.
DOI : 10.1146/annurev.es.25.110194.001321

R. V?-ain?-ol?-a and M. M. Hvilsom, Genetic divergence and a hybrid zone between Baltic and North Sea Mytilus populations (Mytilidae: Mollusca), Biological Journal of the Linnean Society, vol.43, pp.127-148, 1991.

P. M. Visscher, W. G. Hill, and N. R. Wray, Heritability in the genomics era ??? concepts and misconceptions, Nature Reviews Genetics, vol.66, issue.4, pp.255-266, 2008.
DOI : 10.1161/01.HYP.36.2.195

R. S. Waples, Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species, Journal of Heredity, vol.89, issue.5, pp.438-450, 1998.
DOI : 10.1093/jhered/89.5.438

R. S. Waples, Testing for Hardy???Weinberg Proportions: Have We Lost the Plot?, Journal of Heredity, vol.180, issue.2, pp.1-19, 2015.
DOI : 10.1534/genetics.108.089409

R. S. Waples and O. Gaggiotti, What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity, Molecular Ecology, vol.12, issue.6, pp.1419-1439, 2006.
DOI : 10.1515/9781400860180

R. S. Waples, A. E. Punt, and J. M. Cope, Integrating genetic data into management of marine resources: how can we do it better?, Fish and Fisheries, vol.16, issue.Suppl., pp.423-449, 2008.
DOI : 10.1017/S0016672300020553

M. C. Whitlock and D. E. Mccauley, Indirect measures of gene flow and migration: FST???1/(4Nm+1), Heredity, vol.31, issue.2, pp.117-125, 1999.
DOI : 10.1111/j.1558-5646.1990.tb05243.x
URL : https://www.nature.com/articles/6884960.pdf

A. B. Wilson and I. E. Veraguth, The impact of Pleistocene glaciation across the range of a widespread European coastal species, Molecular Ecology, vol.167, issue.20, pp.4535-4553, 2010.
DOI : 10.1111/j.0014-3820.2003.tb00345.x

S. Wright, THE GENETICAL STRUCTURE OF POPULATIONS, Annals of Eugenics, vol.31, issue.111, pp.323-354, 1951.
DOI : 10.2307/2405519

M. Zbawicka, T. Sanko, J. Strand, and R. Wenne, New SNP markers reveal largely concordant clinal variation across the hybrid zone between Mytilus spp. in the Baltic Sea, Aquatic Biology, vol.21, issue.1, pp.25-36, 2014.
DOI : 10.3354/ab00566

, Marine connectivity in the genomic era Gagnaire et al