H. Hoekstra and J. Coyne, THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION, Evolution, vol.428, issue.1, pp.995-1016, 2007.
DOI : 10.1111/j.1558-5646.2007.00105.x

T. Mitchell-olds, J. Willis, and D. Goldstein, Which evolutionary processes influence natural genetic variation for phenotypic traits?, Nature Reviews Genetics, vol.37, issue.11, pp.845-856, 2007.
DOI : 10.1038/nrg2207

J. Stinchcombe and H. Hoekstra, Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits, Heredity, vol.143, issue.2, pp.158-170, 2008.
DOI : 10.1093/jhered/esh012

J. Antonovics, A. Bradshaw, and R. Turner, Heavy Metal Tolerance in Plants, Adv Ecol Res, vol.7, pp.1-85, 1971.
DOI : 10.1016/S0065-2504(08)60202-0

W. Ernst, Schwermetallvegetationen der Erde, 1974.

U. Krä-mer, Metal Hyperaccumulation in Plants, Annual Review of Plant Biology, vol.61, issue.1, pp.517-534, 2010.
DOI : 10.1146/annurev-arplant-042809-112156

N. Verbruggen, C. Hermans, and H. Schat, Molecular mechanisms of metal hyperaccumulation in plants, New Phytologist, vol.159, issue.3, pp.759-776, 2009.
DOI : 10.1111/j.1469-8137.2008.02748.x

M. Hanikenne, I. Talke, M. Haydon, C. Lanz, and A. Nolte, Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4, Nature, vol.13, issue.7193, pp.391-395, 2008.
DOI : 10.1038/nature06877

R. Boyd, Elemental defenses of plants by metals, Nature Education Knowledge, vol.1, issue.6, 2010.

S. Clemens, Molecular mechanisms of plant metal tolerance and homeostasis, Planta, vol.212, issue.4, pp.475-486, 2001.
DOI : 10.1007/s004250000458

M. Becher, I. Talke, L. Krall, and U. Krämer, Cross-species microarray transcript profiling reveals high constitutive expression of metal homeostasis genes in shoots of the zinc hyperaccumulator Arabidopsis halleri, The Plant Journal, vol.39, issue.2, pp.251-268, 2004.
DOI : 10.1046/j.1365-313X.2003.01959.x

I. Talke, M. Hanikenne, and U. Krä-mer, Zinc-Dependent Global Transcriptional Control, Transcriptional Deregulation, and Higher Gene Copy Number for Genes in Metal Homeostasis of the Hyperaccumulator Arabidopsis halleri, PLANT PHYSIOLOGY, vol.142, issue.1, pp.148-167, 2006.
DOI : 10.1104/pp.105.076232

M. Weber, E. Harada, C. Vess, E. Roepenack-lahaye, and S. Clemens, Comparative microarray analysis of Arabidopsis thaliana and Arabidopsis halleri roots identifies nicotianamine synthase, a ZIP transporter and other genes as potential metal hyperaccumulation factors, The Plant Journal, vol.39, issue.2, pp.269-281, 2004.
DOI : 10.1046/j.1365-313X.2003.01960.x

D. Drä-ger, A. Desbrosses-fonrouge, C. Krach, A. Chardonnens, and R. Meyer, transcript levels, The Plant Journal, vol.23, issue.3, pp.425-439, 2004.
DOI : 10.1111/j.1365-313X.2004.02143.x

U. Deinlein, M. Weber, H. Schmidt, S. Rensch, and A. Trampczynska, Elevated Nicotianamine Levels in Arabidopsis halleri Roots Play a Key Role in Zinc Hyperaccumulation, THE PLANT CELL ONLINE, vol.24, issue.2, pp.708-723, 2012.
DOI : 10.1105/tpc.111.095000

Y. Lin, H. Liang, S. Yang, A. Boch, and S. Clemens, Arabidopsis IRT3 is a zinc-regulated and plasma membrane localized zinc/iron transporter, New Phytologist, vol.93, issue.2, pp.392-404, 2009.
DOI : 10.1111/j.1469-8137.2009.02766.x

M. Courbot, G. Willems, P. Motte, S. Arvidsson, and N. Roosens, A Major Quantitative Trait Locus for Cadmium Tolerance in Arabidopsis halleri Colocalizes with HMA4, a Gene Encoding a Heavy Metal ATPase, PLANT PHYSIOLOGY, vol.144, issue.2, pp.1052-1065, 2007.
DOI : 10.1104/pp.106.095133

URL : https://hal.archives-ouvertes.fr/hal-00170435

D. Hussain, M. Haydon, Y. Wang, E. Wong, and S. Sherson, P-Type ATPase Heavy Metal Transporters with Roles in Essential Zinc Homeostasis in Arabidopsis, The Plant Cell, vol.16, issue.5, pp.1327-1339, 2004.
DOI : 10.1105/tpc.020487

G. Willems, D. Drä-ger, M. Courbot, C. Gode, and N. Verbruggen, The Genetic Basis of Zinc Tolerance in the Metallophyte Arabidopsis halleri ssp. halleri (Brassicaceae): An Analysis of Quantitative Trait Loci, Genetics, vol.176, issue.1, pp.659-674, 2007.
DOI : 10.1534/genetics.106.064485

URL : https://hal.archives-ouvertes.fr/hal-00170445

G. Willems, H. Frérot, J. Gennen, P. Salis, and P. Saumitou-laprade, Quantitative trait loci analysis of mineral element concentrations in an Arabidopsis halleri????????Arabidopsis lyrata petraea F2 progeny grown on cadmium-contaminated soil, New Phytologist, vol.181, issue.2, pp.368-379, 2010.
DOI : 10.1111/j.1469-8137.2010.03294.x

URL : https://hal.archives-ouvertes.fr/hal-00489947

H. Frérot, M. Faucon, G. Willems, C. Gode, and A. Courseaux, Genetic architecture of zinc hyperaccumulation in Arabidopsis halleri: the essential role of QTL????????environment interactions, New Phytologist, vol.78, issue.2, pp.355-367, 2010.
DOI : 10.1111/j.1469-8137.2010.03295.x

A. Papoyan and L. Kochian, Identification of Thlaspi caerulescens Genes That May Be Involved in Heavy Metal Hyperaccumulation and Tolerance. Characterization of a Novel Heavy Metal Transporting ATPase, PLANT PHYSIOLOGY, vol.136, issue.3, pp.3814-3823, 2004.
DOI : 10.1104/pp.104.044503

O. 'lochlainn, S. Bowen, H. Fray, R. Hammond, J. King et al., Tandem Quadruplication of HMA4 in the Zinc (Zn) and Cadmium (Cd) Hyperaccumulator Noccaea caerulescens, PLoS ONE, vol.16, issue.3, p.17814, 2011.
DOI : 10.1371/journal.pone.0017814.s016

Z. Shahzad, F. Gosti, H. Frérot, E. Lacombe, and N. Roosens, The Five AhMTP1 Zinc Transporters Undergo Different Evolutionary Fates towards Adaptive Evolution to Zinc Tolerance in Arabidopsis halleri, PLoS Genetics, vol.305, issue.4, p.1000911, 2010.
DOI : 10.1371/journal.pgen.1000911.s004

URL : https://hal.archives-ouvertes.fr/hal-00461837

M. Mirouze, J. Sels, O. Richard, P. Czernic, and S. Loubet, , confers zinc tolerance, The Plant Journal, vol.62, issue.3, pp.329-342, 2006.
DOI : 10.1111/j.1365-313X.2006.02788.x

S. Ohno, Evolution by gene duplication, 1970.
DOI : 10.1007/978-3-642-86659-3

K. Lipinski, J. Farslow, K. Fitzpatrick, M. Lynch, and V. Katju, High Spontaneous Rate of Gene Duplication in Caenorhabditis elegans, Current Biology, vol.21, issue.4, pp.306-310, 2011.
DOI : 10.1016/j.cub.2011.01.026

M. Lynch, W. Sung, K. Morris, N. Coffey, and C. Landry, A genome-wide view of the spectrum of spontaneous mutations in yeast, Proceedings of the National Academy of Sciences, vol.105, issue.27, pp.9272-9277, 2008.
DOI : 10.1073/pnas.0803466105

J. Chen, D. Cooper, N. Chuzhanova, C. Ferec, and G. Patrinos, Gene conversion: mechanisms, evolution and human disease, Nature Reviews Genetics, vol.98, issue.10, pp.762-775, 2007.
DOI : 10.1038/nrg2193

J. Michaelson, Y. Shi, M. Gujral, H. Zheng, and D. Malhotra, Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation, Cell, vol.151, issue.7, pp.1431-1442, 2012.
DOI : 10.1016/j.cell.2012.11.019

M. Lynch and J. Conery, The Evolutionary Fate and Consequences of Duplicate Genes, Science, vol.290, issue.5494, pp.1151-1155, 2000.
DOI : 10.1126/science.290.5494.1151

H. Innan and F. Kondrashov, The evolution of gene duplications: classifying and distinguishing between models, Nature Reviews Genetics, vol.178, issue.4, pp.97-108, 2010.
DOI : 10.1038/nrg2689

R. Michelmore and B. Meyers, Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process, Genome Res, vol.8, pp.1113-1130, 1998.

T. Sutton, U. Baumann, J. Hayes, N. Collins, and B. Shi, Boron-Toxicity Tolerance in Barley Arising from Efflux Transporter Amplification, Science, vol.318, issue.5855, pp.1446-1449, 2007.
DOI : 10.1126/science.1146853

L. Maron, C. Guimaraes, M. Kirst, P. Albert, and J. Birchler, Aluminum tolerance in maize is associated with higher MATE1 gene copy number, Proceedings of the National Academy of Sciences, vol.110, issue.13, pp.5241-5246, 2013.
DOI : 10.1073/pnas.1220766110

G. Perry, N. Dominy, K. Claw, A. Lee, and H. Fiegler, Diet and the evolution of human amylase gene copy number variation, Nature Genetics, vol.16, issue.10, pp.1256-1260, 2007.
DOI : 10.1038/ng2123

F. Kondrashov, Gene duplication as a mechanism of genomic adaptation to a changing environment, Proceedings of the Royal Society B: Biological Sciences, vol.184, issue.4, pp.5048-5057, 2012.
DOI : 10.1534/genetics.109.111963

H. Kubota and C. Takenaka, is a Hyperaccumulator of Cd and Zn, International Journal of Phytoremediation, vol.5, issue.3, pp.197-201, 2003.
DOI : 10.1080/713779219

T. Hu, P. Pattyn, E. Bakker, J. Cao, and J. Cheng, The Arabidopsis lyrata genome sequence and the basis of rapid genome size change, Nature Genetics, vol.537, issue.5, pp.476-481, 2011.
DOI : 10.1006/jmbi.1990.9999

N. Barton, Genetic hitchhiking, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.355, issue.1403, pp.1553-1562, 2000.
DOI : 10.1098/rstb.2000.0716

S. Ramos-onsins, B. Stranger, T. Mitchell-olds, and M. Aguade, Multilocus Analysis of Variation and Speciation in the Closely Related Species Arabidopsis halleri and A. lyrata, Genetics, vol.166, issue.1, pp.373-388, 2004.
DOI : 10.1534/genetics.166.1.373

A. Heidel, S. Ramos-onsins, W. Wang, T. Chiang, and T. Mitchell-olds, Population history in Arabidopsis halleri using multilocus analysis, Molecular Ecology, vol.174, issue.16, pp.3364-3379, 2010.
DOI : 10.1111/j.1365-294X.2010.04761.x

C. Roux, V. Castric, M. Pauwels, S. Wright, and P. Saumitou-laprade, Does Speciation between Arabidopsis halleri and Arabidopsis lyrata Coincide with Major Changes in a Molecular Target of Adaptation?, PLoS ONE, vol.7, issue.11, p.26872, 2011.
DOI : 10.1371/journal.pone.0026872.s013

URL : https://hal.archives-ouvertes.fr/hal-00644381

Y. Fu and W. Li, Statistical tests of neutrality of mutations, Genetics, vol.133, pp.693-709, 1993.

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

M. Purugganan and D. Fuller, The nature of selection during plant domestication, Nature, vol.3, issue.7231, pp.843-848, 2009.
DOI : 10.1038/nature07895

D. Benovoy and G. Drouin, Ectopic gene conversions in the human genome, Genomics, vol.93, issue.1, pp.27-32, 2009.
DOI : 10.1016/j.ygeno.2008.09.007

T. Petes and C. Hill, Recombination Between Repeated Genes in Microorganisms, Annual Review of Genetics, vol.22, issue.1, pp.147-168, 1988.
DOI : 10.1146/annurev.ge.22.120188.001051

C. Casola, G. Conant, and M. Hahn, Very Low Rate of Gene Conversion in the Yeast Genome, Molecular Biology and Evolution, vol.29, issue.12, pp.3817-3826, 2012.
DOI : 10.1093/molbev/mss192

L. Gao and H. Innan, Very Low Gene Duplication Rate in the Yeast Genome, Science, vol.306, issue.5700, pp.1367-1370, 2004.
DOI : 10.1126/science.1102033

J. Kroymann, S. Donnerhacke, D. Schnabelrauch, and T. Mitchell-olds, Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus, Proceedings of the National Academy of Sciences, vol.100, issue.Supplement 2, pp.14587-14592, 2003.
DOI : 10.1073/pnas.1734046100

E. Bosch, M. Hurles, A. Navarro, and M. Jobling, Dynamics of a Human Interparalog Gene Conversion Hotspot, Genome Research, vol.14, issue.5, pp.835-844, 2004.
DOI : 10.1101/gr.2177404

R. Assis and A. Kondrashov, A Strong Deletion Bias in Nonallelic Gene Conversion, PLoS Genetics, vol.426, issue.2, p.1002508, 2012.
DOI : 10.1371/journal.pgen.1002508.s002

C. Casola, U. Zekonyte, A. Phillips, D. Cooper, and M. Hahn, Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease, Genome Research, vol.22, issue.3, pp.429-435, 2012.
DOI : 10.1101/gr.127738.111

H. Innan, A method for estimating the mutation, gene conversion and recombination parameters in small multigene families, Genetics, vol.161, pp.865-872, 2002.

H. Innan, The coalescent and infinite-site model of a small multigene family, Genetics, vol.163, pp.803-810, 2003.

S. Mano and H. Innan, The Evolutionary Rate of Duplicated Genes Under Concerted Evolution, Genetics, vol.180, issue.1, pp.493-505, 2008.
DOI : 10.1534/genetics.108.087676

K. Teshima and H. Innan, The Coalescent with Selection on Copy Number Variants, Genetics, vol.190, issue.3, pp.1077-1086, 2012.
DOI : 10.1534/genetics.111.135343

T. Ohta, On the evolution of multigene families, Theoretical Population Biology, vol.23, issue.2, pp.216-240, 1983.
DOI : 10.1016/0040-5809(83)90015-1

L. Baekgaard, M. Mikkelsen, D. Sorensen, J. Hegelund, and D. Persson, A Combined Zinc/Cadmium Sensor and Zinc/Cadmium Export Regulator in a Heavy Metal Pump, Journal of Biological Chemistry, vol.285, issue.41, pp.31243-31252, 2010.
DOI : 10.1074/jbc.M110.111260

M. Parniske, K. Hammond-kosack, C. Golstein, C. Thomas, and D. Jones, Novel Disease Resistance Specificities Result from Sequence Exchange between Tandemly Repeated Genes at the Cf-4/9 Locus of Tomato, Cell, vol.91, issue.6, pp.821-832, 1997.
DOI : 10.1016/S0092-8674(00)80470-5

H. Kuang, K. Caldwell, B. Meyers, and R. Michelmore, Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximity, The Plant Journal, vol.47, issue.1, pp.69-80, 2008.
DOI : 10.1111/j.1365-313X.2008.03408.x

H. Kuang, S. Woo, B. Meyers, E. Nevo, and R. Michelmore, Multiple Genetic Processes Result in Heterogeneous Rates of Evolution within the Major Cluster Disease Resistance Genes in Lettuce, THE PLANT CELL ONLINE, vol.16, issue.11, pp.2870-2894, 2004.
DOI : 10.1105/tpc.104.025502

M. Mondragon-palomino and B. Gaut, Gene Conversion and the Evolution of Three Leucine-Rich Repeat Gene Families in Arabidopsis thaliana, Molecular Biology and Evolution, vol.22, issue.12, pp.2444-2456, 2005.
DOI : 10.1093/molbev/msi241

J. Bergelson, M. Kreitman, E. Stahl, and D. Tian, Evolutionary Dynamics of Plant R-Genes, Science, vol.292, issue.5525, pp.2281-2285, 2001.
DOI : 10.1126/science.1061337

M. Koch and M. Matschinger, Evolution and genetic differentiation among relatives of Arabidopsis thaliana, Proceedings of the National Academy of Sciences, vol.104, issue.15, pp.6272-6277, 2007.
DOI : 10.1073/pnas.0701338104

M. Dassanayake, D. Oh, J. Haas, A. Hernandez, and H. Hong, The genome of the extremophile crucifer Thellungiella parvula, Nature Genetics, vol.2008, issue.9, pp.913-918, 2011.
DOI : 10.1186/gb-2009-10-3-r25

S. Nair, D. Nash, D. Sudimack, A. Jaidee, and M. Barends, Recurrent Gene Amplification and Soft Selective Sweeps during Evolution of Multidrug Resistance in Malaria Parasites, Molecular Biology and Evolution, vol.24, issue.2, pp.562-573, 2007.
DOI : 10.1093/molbev/msl185

D. Cook, T. Lee, X. Guo, S. Melito, and K. Wang, Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean, Science, vol.338, issue.6111, pp.1206-1209, 2012.
DOI : 10.1126/science.1228746

T. Turner, E. Bourne, V. Wettberg, E. Hu, T. Nuzhdin et al., Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils, Nature Genetics, vol.24, issue.3, pp.260-263, 2010.
DOI : 10.1038/ng.515

R. Sugino and H. Innan, Selection for more of the same product as a force to enhance concerted evolution of duplicated genes, Trends in Genetics, vol.22, issue.12, pp.642-644, 2006.
DOI : 10.1016/j.tig.2006.09.014

V. Bert, M. Macnair, D. Laguérie, P. Saumitou-laprade, P. Petit et al., Zinc tolerance and accumulation in metallicolous and nonmetallicolous populations of Arabidopsis halleri (Brassicaceae), New Phytologist, vol.146, issue.2, pp.225-233, 2000.
DOI : 10.1046/j.1469-8137.2000.00634.x

M. Morel, J. Crouzet, A. Gravot, P. Auroy, and N. Leonhardt, AtHMA3, a P1B-ATPase Allowing Cd/Zn/Co/Pb Vacuolar Storage in Arabidopsis, PLANT PHYSIOLOGY, vol.149, issue.2, pp.894-904, 2009.
DOI : 10.1104/pp.108.130294

R. Bradley and D. Hillis, Recombinant DNA sequences generated by PCR amplification, Molecular Biology and Evolution, vol.14, issue.5, pp.592-593, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025797

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

K. Tamura, D. Peterson, N. Peterson, G. Stecher, and M. Nei, MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011.
DOI : 10.1093/molbev/msr121

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

L. Excoffier and H. 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

C. Ramakers, J. Ruijter, R. Deprez, and A. Moorman, Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data, Neuroscience Letters, vol.339, issue.1, pp.62-66, 2003.
DOI : 10.1016/S0304-3940(02)01423-4

J. Hellemans, G. Mortier, D. Paepe, A. Speleman, F. Vandesompele et al., qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data, Genome Biology, vol.8, issue.2, p.19, 2007.
DOI : 10.1186/gb-2007-8-2-r19

D. Haene, B. Vandesompele, J. Hellemans, and J. , Accurate and objective copy number profiling using real-time quantitative PCR, Methods, vol.50, pp.262-270, 2010.

J. Vandesompele, D. Preter, K. Pattyn, F. Poppe, B. et al., Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol, vol.3, p.34, 2002.