R. Amara, T. Meziane, C. Gilliers, G. Hermel, and P. Laffargue, Growth and condition indices in juvenile sole Solea solea measured to assess the quality of essential fish habitat, Marine Ecology Progress Series, vol.351, pp.201-208, 2007.
DOI : 10.3354/meps07154

URL : https://hal.archives-ouvertes.fr/hal-00481472

T. Antao, A. Pérez-figueroa, and G. Luikart, Early detection of population declines: high power of genetic monitoring using effective population size estimators, Evolutionary Applications, vol.38, issue.1, pp.144-154, 2011.
DOI : 10.1111/j.1752-4571.2010.00150.x

E. Aro, A review of fish migration patterns in the Baltic, Rapp P-V Cons Int Explor Mer, vol.190, pp.72-96, 1989.

J. Avise, Molecular markers, natural history and evolution, 1994.
DOI : 10.1007/978-1-4615-2381-9

J. Ballard and R. Melvin, Linking the mitochondrial genotype to the organismal phenotype, Molecular Ecology, vol.37, issue.8, pp.1523-1539, 2010.
DOI : 10.1111/j.1365-294X.2010.04594.x

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, 1996.

P. Borsa, A. Blanquer, and P. Berrebi, Genetic structure of the flounders Platichthys flesus and P. stellatus at different geographic scales, Marine Biology, vol.129, issue.2, pp.233-246, 1997.
DOI : 10.1007/s002270050164

J. Brookfield, A simple new method for estimating null allele frequency from heterozygote deficiency, Molecular Ecology, vol.4, issue.3, pp.453-455, 1996.
DOI : 10.2307/2408474

H. Cabral, M. Costa, and J. Salgado, Does the Tagus estuary fish community reflect environmental changes?, Climate Research, vol.18, pp.119-126, 2001.
DOI : 10.3354/cr018119

H. Cabral, R. Vasconcelos, C. Vinagre, S. França, and . Others, Relative importance of estuarine flatfish nurseries along the Portuguese coast, Journal of Sea Research, vol.57, issue.2-3, pp.209-217, 2007.
DOI : 10.1016/j.seares.2006.08.007

J. Cachot, O. Geffard, S. Augagneur, S. Lacroix, and . Others, Evidence of genotoxicity related to high PAH content of sediments in the upper part of the Seine estuary (Normandy, France), Aquatic Toxicology, vol.79, issue.3, pp.257-267, 2006.
DOI : 10.1016/j.aquatox.2006.06.014

P. Casas, P. Martinez, and L. Sanchez, Characterization of microsatellite markers derived from sequence databases for the European flounder (Platichthys flesus), Molecular Ecology Notes, vol.1, issue.3, pp.664-665, 2005.
DOI : 10.1007/s002270050164

L. Cavalli-sforza and A. Edwards, Phylogenetic Analysis: Models and Estimation Procedures, Evolution, vol.21, issue.3, pp.550-570, 1967.
DOI : 10.2307/2406616

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1706274

E. Chang, M. Menezes, N. Meyer, R. Cucci, V. Vervoort et al., and its phenotypic consequences, Human Mutation, vol.33, issue.6, pp.582-589, 2004.
DOI : 10.1002/humu.20048

A. Chapman and D. Atkinson, Stabilization of adenylate energy charge by the adenylate reaction, J Biol Chem, vol.248, pp.8309-8312, 1973.

M. Clement, D. Posada, and K. Crandall, TCS: a computer program to estimate gene genealogies, Molecular Ecology, vol.11, issue.10, pp.1657-1659, 2000.
DOI : 10.1046/j.1365-294x.2000.01020.x

K. Crandall, A. Templeton, and C. Sing, Intraspecific phylogenetics: problems and solutions (eds) Models in phylogeny reconstruction, Systematics Association Special Vol, vol.52, pp.273-297, 1994.

P. Dando, Site fidelity, homing and spawning migrations of flounder Platichthys flesus in the Tamar estuary, South West England, Marine Ecology Progress Series, vol.430, pp.183-196, 2011.
DOI : 10.3354/meps09116

D. Hardie and J. Hutchings, Evolutionary ecology at the extremes of species??? ranges, Environmental Reviews, vol.18, issue.NA, pp.1-20, 2010.
DOI : 10.1139/A09-014

C. Harley, A. Hughes, K. Hultgren, B. Miner, and . Others, The impacts of climate change in coastal marine systems, Ecology Letters, vol.30, issue.Suppl. 1, pp.228-241, 2006.
DOI : 10.1111/j.1461-0248.2005.00871.x

J. Hemmer-hansen, E. Nielsen, P. Gronkjaer, and V. Loeschcke, L.), Molecular Ecology, vol.28, issue.15, pp.3104-3118, 2007.
DOI : 10.1111/j.1365-294X.2007.03367.x

J. Hemmer-hansen, E. Nielsen, J. Frydenberg, and V. Loeschcke, Adaptive divergence in a high gene flow environment: Hsc70 variation in the European flounder (Platichthys flesus L.), Heredity, vol.29, issue.6, pp.592-600, 2007.
DOI : 10.1111/j.1432-1033.1992.tb16709.x

M. Hermant, J. Lobry, S. Bonhommeau, J. Poulard, L. Pape et al., Impact of warming on abundance and occurrence of flatfish populations in the Bay of Biscay (France), Journal of Sea Research, vol.64, issue.1-2, pp.45-53, 2010.
DOI : 10.1016/j.seares.2009.07.001

URL : https://hal.archives-ouvertes.fr/hal-00494573

J. Hutchings, D. Swain, S. Rowe, J. Eddington, V. Puvanendran et al., Genetic variation in life-history reaction norms in a marine fish, Proceedings of the Royal Society B: Biological Sciences, vol.84, issue.5, pp.1693-16990263, 2007.
DOI : 10.1093/jhered/89.5.438

R. Ihaka and R. Gentleman, R: a language for data analysis and graphics, J Comput Graph Statist, vol.5, pp.299-314, 1996.

N. Ivanova, J. De-waard, and P. Hebert, An inexpensive, automation-friendly protocol for recovering high-quality DNA, Molecular Ecology Notes, vol.360, issue.4, pp.998-1002, 2006.
DOI : 10.1111/j.1471-8286.2006.01428.x

S. Karlsson and J. Mork, Deviation from Hardy???Weinberg equilibrium, and temporal instability in allele frequencies at microsatellite loci in a local population of Atlantic cod, ICES Journal of Marine Science, vol.62, issue.8, 2005.
DOI : 10.1016/j.icesjms.2005.05.009

R. Kelly and D. Eernisse, SOUTHERN HOSPITALITY: A LATITUDINAL GRADIENT IN GENE FLOW IN THE MARINE ENVIRONMENT, Evolution, vol.15, issue.3, pp.700-707, 2007.
DOI : 10.1111/j.1365-294X.2006.02911.x

M. Larmuseau, J. Raeymaekers, H. Hellemans, V. Houdt, J. Volckaert et al., Mito-nuclear discordance in the degree of population differentiation in a marine goby, Heredity, vol.121, issue.6, pp.532-542, 2010.
DOI : 10.2307/2408641

P. Larsen, E. Nielsen, T. Williams, J. Hemmer-hansen, and . Others, Adaptive differences in gene expression in European flounder (Platichthys flesus), Molecular Ecology, vol.288, issue.22, pp.4674-4683, 2007.
DOI : 10.1016/j.ygcen.2006.05.006

J. Lowenstein, Ammonia production in muscle and other tissues: the purine nucleotide cycle, Physiol Rev, vol.52, pp.382-414, 1972.

N. Mantel, The detection of disease clustering and a generalized regression approach, Cancer Res, vol.27, pp.209-220, 1967.

J. Marchand, A. Tanguy, J. Laroche, L. Quiniou, and D. Moraga, Responses of European flounder Platichthys flesus populations to contamination in different estuaries along the Atlantic coast of France, Marine Ecology Progress Series, vol.260, pp.273-284, 2003.
DOI : 10.3354/meps260273

J. Marchand, L. Quiniou, R. Riso, M. Thébaut, and J. Laroche, Physiological cost of tolerance to toxicants in the European flounder Platichthys flesus, along the French Atlantic Coast, Aquatic Toxicology, vol.70, issue.4, pp.327-343, 2004.
DOI : 10.1016/j.aquatox.2004.10.001

J. Marchand, E. Evrard, B. Guinand, J. Cachot, L. Quiniou et al., Genetic polymorphism and its potential relation to environmental stress in five populations of the European flounder Platichthys flesus, along the French Atlantic coast, Marine Environmental Research, vol.70, issue.2, pp.201-209, 2010.
DOI : 10.1016/j.marenvres.2010.05.002

URL : https://hal.archives-ouvertes.fr/hal-00602600

A. Meistertzheim, I. Calves, S. Artigaud, C. Friedman, J. Laroche et al., High Resolution Melting Analysis for fast and cheap polymorphism screening of marine populations, Protocol Exchange, p.15, 2012.
DOI : 10.1038/protex.2012.015

A. Menesguen, A. Aminot, C. Belin, A. Chapelle, and . Others, L'eutrophisation des eaux marines et saumâtres en Europe en particulier en France, 2001.

P. Morais, E. Dias, J. Babaluk, and C. Antunes, The migration patterns of the European flounder Platichthys flesus (Linnaeus, 1758) (Pleuronectidae, Pisces) at the southern limit of its distribution range: Ecological implications and fishery management, Journal of Sea Research, vol.65, issue.2, pp.235-246, 2011.
DOI : 10.1016/j.seares.2010.11.001

M. Moran, Arguments for rejecting the sequential Bonferroni in ecological studies, Oikos, vol.100, issue.2, pp.403-405, 2003.
DOI : 10.1034/j.1600-0706.2003.12010.x

C. Munschy, K. Mosan, I. Truquet, and J. Tronczynski, Caractérisation chimique de la contamination organique dans l'estuaire de la Seine. Rapport Seine-Aval 1996, 1997.

E. Nielsen, P. Nielsen, D. Meldrup, M. Hansen, and J. Wright, 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 Microsatellite DNA in fishes, Mol Ecol Rev Fish Biol Fish, vol.13, issue.7, pp.585-595331, 1997.

O. Connor, M. Bruno, J. Gaines, S. Halpern, B. Lester et al., Temperature control of larval dispersal and the implications for marine ecology, evolution, and conservation, Proceedings of the National Academy of Sciences, vol.104, issue.4, pp.1266-1271, 2007.
DOI : 10.1073/pnas.0603422104

E. Olsen, H. Knutsen, J. Gjosaeter, P. Jorde, J. Knutsen et al., Small-scale biocomplexity in coastal Atlantic cod supporting a Darwinian perspective on fisheries management, Evolutionary Applications, vol.62, issue.Suppl 1, pp.524-533, 2008.
DOI : 10.1111/j.1752-4571.2008.00024.x

D. Posada, jModelTest: Phylogenetic Model Averaging, Molecular Biology and Evolution, vol.25, issue.7, pp.1253-1256, 2008.
DOI : 10.1093/molbev/msn083

URL : http://mbe.oxfordjournals.org/cgi/content/short/25/7/1253

A. Pulsford, K. Ryan, and J. Nott, Metals and melanomacrophages in flounder, Platichthys flesus, spleen and kidney, Journal of the Marine Biological Association of the United Kingdom, vol.716, issue.02, pp.483-498, 1992.
DOI : 10.1111/j.1365-2761.1985.tb01195.x

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

J. Roman and S. Palumbi, A global invader at home: population structure of the green crab, Carcinus maenas, in Europe, Molecular Ecology, vol.191, issue.10, pp.2891-2898, 2004.
DOI : 10.1111/j.1365-294X.2004.02255.x

F. Rousset, genepop???007: a complete re-implementation of the genepop software for Windows and Linux, Molecular Ecology Resources, vol.145, issue.1, pp.103-106, 2008.
DOI : 10.2307/2408641

URL : https://hal.archives-ouvertes.fr/halsde-00366752

M. Schuelke, An economic method for the fluorescent labeling of PCR fragments, Nature Biotechnology, vol.252, issue.2, pp.233-234, 2000.
DOI : 10.1038/72708

M. Schwartz, G. Luikart, and R. Waples, Genetic monitoring as a promising tool for conservation and management, Trends in Ecology & Evolution, vol.22, issue.1, pp.25-33, 2007.
DOI : 10.1016/j.tree.2006.08.009

C. Sgro, A. Lowe, and A. Hoffmann, Building evolutionary resilience for conserving biodiversity under climate change, Evolutionary Applications, vol.270, issue.2, pp.326-337, 2011.
DOI : 10.1111/j.1752-4571.2010.00157.x

M. Slatkin, A measure of population subdivision based on microsatellite allele frequencies, Genetics, vol.139, pp.457-462, 1995.

J. Storey, A direct approach to false discovery rates, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol.82, issue.3, pp.479-498, 2002.
DOI : 10.1111/1467-9868.00346

R. Summers, (L.) in the Ythan estuary, Scotland, Journal of Natural History, vol.4, issue.5, pp.703-723, 1979.
DOI : 10.1017/S0025315400054448

URL : https://hal.archives-ouvertes.fr/in2p3-00006092

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

A. Templeton, K. Crandall, and C. Sing, A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data, 1992.

M. Thébault, A. Tanguy, A. Meistertzheim, and J. Raffin, Partial characterization of the gene encoding myoadenylate deaminase from the teleost fish Platichthys flesus, Fish Physiology and Biochemistry, vol.69, issue.4, pp.819-825, 2010.
DOI : 10.1007/s10695-009-9358-y

R. Thiel, H. Cabral, and M. Costa, Composition, temporal changes and ecological guild classification of the ichthyofaunas of large European estuaries - a comparison between the Tagus (Portugal) and the Elbe (Germany), Journal of Applied Ichthyology, vol.58, issue.5, pp.330-342, 2003.
DOI : 10.1007/s002270000491

N. Tysklind, T. Neuparth, G. Ashcroft, M. Taylor, B. Lyons et al., L.), Molecular Ecology Resources, vol.90, issue.3, pp.1065-1068, 2009.
DOI : 10.1111/j.1755-0998.2009.02589.x

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

R. Waples and C. Do, using highly variable genetic markers: a largely untapped resource for applied conservation and evolution, Evolutionary Applications, vol.180, issue.Special issue 1, pp.244-262, 2010.
DOI : 10.1111/j.1752-4571.2009.00104.x

R. Ward, T. Zemlak, B. Innes, P. Last, and P. Hebert, DNA barcoding Australia's fish species, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.11, issue.6897, pp.1847-1857, 2005.
DOI : 10.1093/molbev/msg133

A. Was, E. Gosling, and G. Hoarau, Microsatellite analysis of plaice (Pleuronectes platessa L.) in the NE Atlantic: weak genetic structuring in a milieu of high gene flow, Marine Biology, vol.38, issue.3, pp.447-462, 2010.
DOI : 10.1007/s00227-009-1331-x

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

M. Yoshino and K. Muramaki, In situ studies on AMP deaminase as a control system of the adenylate energy charge in yeasts, Biochimica et Biophysica Acta (BBA) - General Subjects, vol.672, issue.1, pp.16-20, 1981.
DOI : 10.1016/0304-4165(81)90274-9