V. Llaurens, A. Whibley, and M. Joron, Genetic architecture and balancing selection: the life and death of differentiated variants, Mol Ecol, vol.26, issue.9, pp.2430-2478, 2017.

T. Schwander, R. Libbrecht, and L. Keller, Supergenes and complex phenotypes, Curr Biol, vol.24, issue.7, pp.288-94, 2014.

M. J. Thompson and C. D. Jiggins, Supergenes and their role in evolution, Heredity, vol.113, issue.1, pp.1-8, 2014.

A. D. Twyford and J. Friedman, Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion, Evolution, vol.69, issue.6, pp.1476-86, 2015.

K. Hermann, U. Klahre, M. Moser, H. Sheehan, T. Mandel et al., Tight genetic linkage of prezygotic barrier loci creates a multifunctional speciation island in Petunia, Curr Biol, vol.23, issue.10, pp.873-880, 2013.

R. A. Fisher, The genetical theory of natural selection, 1930.

M. Joron, L. Frezal, R. T. Jones, N. L. Chamberlain, S. F. Lee et al., Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry, Nature, vol.477, issue.7363, pp.203-209, 2011.

L. P. Lawson, R. K. Vander-meer, and D. Shoemaker, Male reproductive fitness and queen polyandry are linked to variation in the supergene Gp-9 in the fire ant Solenopsis invicta, Proc Biol Sci, vol.279, pp.3217-3239, 1741.

A. C. Brennan, Distyly supergenes as a model to understand the evolution of genetic architecture, Am J Bot, vol.104, issue.1, pp.5-7, 2017.

C. Küpper, M. Stocks, J. E. Risse, D. Remedios, N. Farrell et al., A supergene determines highly divergent male reproductive morphs in the ruff, Nat Genet, vol.48, issue.1, pp.79-83, 2016.

E. M. Tuttle, A. O. Bergland, M. L. Korody, M. S. Brewer, D. J. Newhouse et al., Divergence and functional degradation of a sex chromosome-like supergene, Curr Biol, vol.26, issue.3, pp.344-50, 2016.

T. G. Kirubakaran, H. Grove, M. P. Kent, S. R. Sandve, M. Baranski et al., Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod, Mol Ecol, vol.25, issue.10, pp.2130-2173, 2016.

M. J. Wheeler, B. H. De-graaf, N. Hadjiosif, R. M. Perry, N. S. Poulter et al., Identification of the pollen self-incompatibility determinant in Papaver rhoeas, Nature, vol.459, issue.7249, pp.992-997, 2009.

J. Li, J. M. Cocker, J. Wright, M. A. Webster, M. Mcmullan et al., Genetic architecture and evolution of the S locus supergene in Primula vulgaris, Nat Plants, vol.2, issue.12, p.16188, 2016.

K. Kunte, W. Zhang, A. Tenger-trolander, D. H. Palmer, A. Martin et al., Doublesex is a mimicry supergene, Nature, vol.507, issue.7491, pp.229-261, 2014.

R. M. Merrill, K. K. Dasmahapatra, J. W. Davey, D. D. Dell'-aglio, J. J. Hanly et al., The diversification of Heliconius butterflies: what have we learned in 150 years?, J Evol Biol, vol.28, issue.8, pp.1417-1455, 2015.

N. Wahlberg, J. Leneveu, U. Kodandaramaiah, C. Peña, S. Nylin et al., Nymphalid butterflies diversify following near demise at the Cretaceous/Tertiary boundary, Proc Biol Sci, vol.276, pp.4295-302, 1677.

N. J. Nadeau, Genes controlling mimetic colour pattern variation in butterflies, Curr Opin Insect Sci, vol.17, pp.24-31, 2016.

R. D. Reed, R. Papa, A. Martin, H. M. Hines, B. A. Counterman et al., Optix drives the repeated convergent evolution of butterfly wing pattern mimicry, Science, vol.333, issue.6046, pp.1137-1178, 2011.

N. J. Nadeau, C. Pardo-diaz, A. Whibley, M. A. Supple, S. V. Saenko et al., The gene cortex controls mimicry and crypsis in butterflies and moths, Nature, vol.534, issue.7605, pp.106-116, 2016.

E. L. Westerman, N. W. Vankuren, D. Massardo, A. Tenger-trolander, W. Zhang et al., Aristaless controls butterfly wing color variation used in mimicry and mate choice, Curr Biol, vol.28, issue.21, pp.3469-74, 2018.

A. Martin, R. Papa, N. J. Nadeau, R. I. Hill, B. A. Counterman et al., Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand, Proc Natl Acad Sci USA, vol.109, issue.31, pp.12632-12639, 2012.

A. Mazo-vargas, C. Concha, L. Livraghi, D. Massardo, R. Wallbank et al., Macroevolutionary shifts of WntA function potentiate butterfly wing-pattern diversity, Proc Natl Acad Sci, vol.114, issue.40, pp.10701-10707, 2017.

L. Zhang, A. Mazo-vargas, and R. D. Reed, Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence, Proc Natl Acad Sci, vol.114, issue.40, pp.10707-10719, 2017.

M. Joron, I. R. Wynne, G. Lamas, and J. Mallet, Variable selection and the coexistence of multiple mimetic forms of the butterfly Heliconius numata, Evol Ecol, vol.13, pp.721-54, 1999.
URL : https://hal.archives-ouvertes.fr/halsde-00342850

M. Joron, R. Papa, M. Beltrán, N. Chamberlain, J. Mavárez et al., A conserved supergene locus controls colour pattern diversity in Heliconius butterflies, PLoS Biol, vol.4, issue.10, p.303, 2006.

T. Dobzhansky, Genetics of the evolutionary process, 1970.

M. Chouteau, V. Llaurens, F. Piron-prunier, and M. Joron, Polymorphism at a mimicry supergene maintained by opposing frequency-dependent selection pressures, Proc Natl Acad Sci, vol.114, issue.31, pp.8325-8334, 2017.

E. Afgan, D. Baker, B. Batut, M. Van-den-beek, D. Bouvier et al., The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update, Nucl Acids Res, vol.46, issue.W1, pp.537-581, 2018.

R. Schmieder and R. Edwards, Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, pp.863-867, 2011.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet J, vol.17, issue.1, pp.10-12, 2011.

R. Schmieder, Y. W. Lim, and R. Edwards, Identification and removal of ribosomal RNA sequences from metatranscriptomes, Bioinformatics, vol.28, issue.3, pp.433-438, 2012.

M. G. Grabherr, B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat Biotechnol, vol.29, issue.7, pp.644-52, 2011.

B. Li and C. N. Dewey, :323. ? fast, convenient online submission ? thorough peer review by experienced researchers in your field ? rapid publication on acceptance ? support for research data, including large and complex data types ? gold Open Access which fosters wider collaboration and increased citations maximum visibility for your research: over 100M website views per year ? At BMC, BMC Bioinform, vol.12, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01153354

R. J. Challis, S. Kumar, K. K. Dasmahapatra, C. D. Jiggins, and M. Blaxter, Lepbase: the Lepidopteran genome database, bioRxiv, vol.1, 2016.

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, pp.357-366, 2012.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., 1000 Genome project data processing subgroup. The sequence alignment/ map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.

N. J. Schurch, P. Schofield, M. Gierli?ski, C. Cole, A. Sherstnev et al., How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?, RNA, vol.22, issue.6, pp.839-51, 2016.

A. Subramanian, P. Tamayo, V. K. Mootha, S. Mukherjee, B. L. Ebert et al., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, PNAS, vol.102, issue.43, pp.15545-50, 2005.

A. Martin and R. D. Reed, Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems, Dev Biol, vol.395, issue.2, pp.367-78, 2014.

J. W. Davey, M. Chouteau, S. L. Barker, L. Maroja, S. W. Baxter et al., Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution. G3 (Bethesda), vol.6, pp.695-708, 2016.

K. M. Kozak, N. Wahlberg, A. F. Neild, K. K. Dasmahapatra, J. Mallet et al., Multilocus species trees show the recent adaptive radiation of the mimetic heliconius butterflies, Syst Biol, vol.64, issue.3, pp.505-529, 2015.

P. Beldade and C. M. Peralta, Developmental and evolutionary mechanisms shaping butterfly eyespots, Curr Opin Insect Sci, vol.19, pp.22-31, 2017.

A. E. Van't-hof, P. Campagne, D. J. Rigden, C. J. Yung, J. Lingley et al., The industrial melanism mutation in British peppered moths is a transposable element, Nature, vol.534, issue.7605, pp.102-107, 2016.

R. W. Wallbank, S. W. Baxter, C. Pardo-diaz, J. J. Hanly, S. H. Martin et al., Evolutionary novelty in a butterfly wing pattern through enhancer shuffling, PLoS Biol, vol.14, issue.1, p.1002353, 2016.

R. B. Hough, A. Lengeling, V. Bedian, C. Lo, and M. Bu?an, Rump white inversion in the mouse disrupts dipeptidyl aminopeptidase-like protein 6 and causes dysregulation of Kit expression, Proc Natl Acad Sci, vol.95, issue.23, pp.13800-13805, 1998.

M. Puig, M. Cáceres, and A. Ruiz, Silencing of a gene adjacent to the breakpoint of a widespread Drosophila inversion by a transposon-induced antisense RNA, Proc Natl Acad Sci USA, vol.101, issue.24, pp.9013-9021, 2004.

, Publisher's Note

, Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations